RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

Searching..................................................done

Query= gi|255764505|ref|YP_003065248.2| polysialic acid capsule
expression protein [Candidatus Liberibacter asiaticus str. psy62]
         (341 letters)



>gnl|CDD|31137 COG0794, GutQ, Predicted sugar phosphate isomerase involved in
           capsule formation [Cell envelope biogenesis, outer
           membrane].
          Length = 202

 Score =  210 bits (535), Expect = 6e-55
 Identities = 100/201 (49%), Positives = 124/201 (61%), Gaps = 4/201 (1%)

Query: 27  ALRSIIAEKRGLSSLESSLQGELSFQFHCAVEKIKAIKGRVVITGIGKSGHIGSKLASTL 86
           A   ++ E   L  L   L  E    F  AVE I   KG+V +TG+GKSG IG K A+ L
Sbjct: 5   AKEILMTEAEALLELAERLDDE---DFVRAVELILECKGKVFVTGVGKSGLIGKKFAARL 61

Query: 87  ASTGTPSFFVHAAEASHGDLGMITRDDLIIVLSWSGSSDELKAILYYARRFSIPLIAITS 146
           ASTGTP+FFV  AEA HGDLGMIT  D++I +S SG + EL  +   A+R    LIAITS
Sbjct: 62  ASTGTPAFFVGPAEALHGDLGMITPGDVVIAISGSGETKELLNLAPKAKRLGAKLIAITS 121

Query: 147 ENKSVVACHADIVLTLPKEPESCPHGLAPTTSAIMQLAIGDALAIALLESRNFSENDFYV 206
              S +A  AD+VL +P + E+CP GLAPTTS  + LA+GDALA  L E+R FS  DF +
Sbjct: 122 NPDSSLAKAADVVLVIPVKTEACPLGLAPTTSTTLTLALGDALAGTLFEARGFSFEDFAI 181

Query: 207 LHPGGKLG-TLFVCASDVMHS 226
            HPGG LG  L +   D M+ 
Sbjct: 182 AHPGGALGAKLLLKVKDHMNL 202


>gnl|CDD|88409 cd05014, SIS_Kpsf, KpsF-like protein. KpsF is an
           arabinose-5-phosphate isomerase which contains SIS
           (Sugar ISomerase) domains. SIS domains are found in many
           phosphosugar isomerases and phosphosugar binding
           proteins. KpsF catalyzes the reversible reaction of
           ribulose 5-phosphate to arabinose 5-phosphate. This is
           the second step in the CMP-Kdo biosynthesis pathway..
          Length = 128

 Score =  174 bits (443), Expect = 3e-44
 Identities = 73/128 (57%), Positives = 96/128 (75%)

Query: 65  GRVVITGIGKSGHIGSKLASTLASTGTPSFFVHAAEASHGDLGMITRDDLIIVLSWSGSS 124
           G+VV+TG+GKSGHI  K+A+TL+STGTP+FF+H  EA HGDLGM+T  D++I +S SG +
Sbjct: 1   GKVVVTGVGKSGHIARKIAATLSSTGTPAFFLHPTEALHGDLGMVTPGDVVIAISNSGET 60

Query: 125 DELKAILYYARRFSIPLIAITSENKSVVACHADIVLTLPKEPESCPHGLAPTTSAIMQLA 184
           DEL  +L + +R   P+IAIT    S +A  +D+VL LP E E+CP GLAPTTS    LA
Sbjct: 61  DELLNLLPHLKRRGAPIIAITGNPNSTLAKLSDVVLDLPVEEEACPLGLAPTTSTTAMLA 120

Query: 185 IGDALAIA 192
           +GDALA+A
Sbjct: 121 LGDALAVA 128


>gnl|CDD|73104 cd04604, CBS_pair_KpsF_GutQ_assoc, This cd contains two tandem
           repeats of the cystathionine beta-synthase (CBS pair)
           domains associated with KpsF/GutQ domains in the API
           [A5P (D-arabinose 5-phosphate) isomerase] protein.
           These APIs catalyze the conversion of the pentose
           pathway intermediate D-ribulose 5-phosphate into A5P, a
           precursor of 3-deoxy-D-manno-octulosonate, which is an
           integral carbohydrate component of various glycolipids
           coating the surface of the outer membrane of
           Gram-negative bacteria, including lipopolysaccharide and
           many group 2 K-antigen capsules. CBS is a small domain
           originally identified in cystathionine beta-synthase and
           subsequently found in a wide range of different
           proteins. CBS domains usually come in tandem repeats,
           which associate to form a so-called Bateman domain or a
           CBS pair which is reflected in this model.  The
           interface between the two CBS domains forms a cleft that
           is a potential ligand binding site. The CBS pair
           coexists with a variety of other functional domains. It
           has been proposed that the CBS domain may play a
           regulatory role, although its exact function is
           unknown..
          Length = 114

 Score =  128 bits (323), Expect = 3e-30
 Identities = 51/113 (45%), Positives = 70/113 (61%), Gaps = 2/113 (1%)

Query: 227 GDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHK--DLNTLS 284
           GD++PLV     L DA+  +S K  G  AVVDE  +L GI T+GD+ R   K  D+ TL 
Sbjct: 1   GDALPLVSPDTSLKDALLEMSRKGLGMTAVVDEDGRLVGIFTDGDLRRALEKGLDILTLP 60

Query: 285 VEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
           V DVM +NPK I  D L   A++L+ ++ I+ L VVDD  + +G++H  DLLR
Sbjct: 61  VADVMTRNPKTIDPDALAAEALELMEENKITALPVVDDNGRPVGVLHIHDLLR 113


>gnl|CDD|144827 pfam01380, SIS, SIS domain.  SIS (Sugar ISomerase) domains are
           found in many phosphosugar isomerases and phosphosugar
           binding proteins. SIS domains are also found in proteins
           that regulate the expression of genes involved in
           synthesis of phosphosugars. Presumably the SIS domains
           bind to the end-product of the pathway.
          Length = 131

 Score = 94.7 bits (236), Expect = 4e-20
 Identities = 48/132 (36%), Positives = 66/132 (50%), Gaps = 4/132 (3%)

Query: 62  AIKGRVVITGIGKSGHIGSKLASTLASTGTPSFFVH-AAEASHGDLGMITRDDLIIVLSW 120
           A   R+ + G G S     +LA  L   G     V  A+E  HG L ++  DDL+I +S 
Sbjct: 3   AKAKRIYVIGAGTSYAAALELALKLEEIGYIVVEVEDASEFRHGPLALVDPDDLVIAISQ 62

Query: 121 SGSSDELKAILYYARRFSIPLIAITSENKSVVACHADIVLTLPKEPESCPHGLAPTTSAI 180
           SG + +L       +     +IAIT    S +A  AD VL +   PE+   G+A T S  
Sbjct: 63  SGETRDLLEAAKLLKARGAKIIAITDSKGSPLAREADHVLYIIAGPEA---GVASTKSLT 119

Query: 181 MQLAIGDALAIA 192
           +QLA+ DALAIA
Sbjct: 120 LQLALLDALAIA 131


>gnl|CDD|31923 COG1737, RpiR, Transcriptional regulators [Transcription].
          Length = 281

 Score = 80.8 bits (199), Expect = 5e-16
 Identities = 47/147 (31%), Positives = 69/147 (46%), Gaps = 3/147 (2%)

Query: 52  QFHCAVEKIKAIKGRVVITGIGKSGHIGSKLASTLASTGTPSFFVHAAEASHGDLGMITR 111
               AVE +   + R+   G+G SG + S LA  L   G     +         L ++T 
Sbjct: 119 ALERAVELLAKAR-RIYFFGLGSSGLVASDLAYKLMRIGLNVVALSDTHGQLMQLALLTP 177

Query: 112 DDLIIVLSWSGSSDELKAILYYARRFSIPLIAITSENKSVVACHADIVLTLPKEPESCPH 171
            D++I +S+SG + E+      A+     +IAIT    S +A  ADIVL +P   ES   
Sbjct: 178 GDVVIAISFSGYTREIVEAAELAKERGAKVIAITDSADSPLAKLADIVLLVPVAEESFFR 237

Query: 172 GLAPTTSAIMQLAIGDALAIALLESRN 198
              P +S I QLA+ DAL  A+ + R 
Sbjct: 238 S--PISSRIAQLALIDALITAVAQRRG 262


>gnl|CDD|73081 cd02205, CBS_pair, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 113

 Score = 80.2 bits (197), Expect = 8e-16
 Identities = 35/111 (31%), Positives = 57/111 (51%), Gaps = 2/111 (1%)

Query: 230 IPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNF--HKDLNTLSVED 287
           +  V     + +A+ ++ E     + VVD+  +L GI+TE D+ R          ++V D
Sbjct: 3   VVTVSPDDTVAEALRLMLEHGISGLPVVDDDGRLVGIVTERDLLRALAEGGLDPLVTVGD 62

Query: 288 VMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
           VM ++   +  DT L  A +L+ +H I  L VVDD  + +GIV   D+LR 
Sbjct: 63  VMTRDVVTVSPDTSLEEAAELMLEHGIRRLPVVDDEGRLVGIVTRSDILRA 113



 Score = 42.1 bits (98), Expect = 2e-04
 Identities = 18/48 (37%), Positives = 28/48 (58%)

Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
           ++   +  D  +  A++L+ +H IS L VVDD  + +GIV   DLLR 
Sbjct: 1   RDVVTVSPDDTVAEALRLMLEHGISGLPVVDDDGRLVGIVTERDLLRA 48


>gnl|CDD|73122 cd04623, CBS_pair_10, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 113

 Score = 72.8 bits (179), Expect = 1e-13
 Identities = 33/109 (30%), Positives = 53/109 (48%), Gaps = 4/109 (3%)

Query: 233 VKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFH---KDLNTLSVEDVM 289
           V+    + +A  +++EK  G V VVD+G +L GI +E DI R             V ++M
Sbjct: 6   VRPDATVAEAAKLMAEKNIGAVVVVDDGGRLVGIFSERDIVRKVALRGASALDTPVSEIM 65

Query: 290 IKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
            +N   +  D  +  AM L+ +     L VVD   K +GIV   D+++ 
Sbjct: 66  TRNVITVTPDDTVDEAMALMTERRFRHLPVVDG-GKLVGIVSIGDVVKA 113



 Score = 32.8 bits (75), Expect = 0.13
 Identities = 13/43 (30%), Positives = 24/43 (55%)

Query: 295 VILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
            +  D  +  A +L+ + NI  ++VVDD  + +GI    D++R
Sbjct: 5   TVRPDATVAEAAKLMAEKNIGAVVVVDDGGRLVGIFSERDIVR 47


>gnl|CDD|88408 cd05013, SIS_RpiR, RpiR-like protein. RpiR contains a SIS (Sugar
           ISomerase) domain, which is found in many phosphosugar
           isomerases and phosphosugar binding proteins. In E.
           coli, rpiR negatively regulates the expression of rpiB
           gene. Both rpiB and rpiA are ribose phosphate isomerases
           that catalyze the reversible reactions of ribose
           5-phosphate into ribulose 5-phosphate..
          Length = 139

 Score = 70.7 bits (173), Expect = 6e-13
 Identities = 42/137 (30%), Positives = 62/137 (45%), Gaps = 3/137 (2%)

Query: 56  AVEKIKAIKGRVVITGIGKSGHIGSKLASTLASTGTPSFFVHAAEASHGDLGMITRDDLI 115
           AV+ +     R+ I G+G SG +   LA  L   G P   +            +T  D++
Sbjct: 6   AVDLLAK-ARRIYIFGVGSSGLVAEYLAYKLLRLGKPVVLLSDPHLQLMSAANLTPGDVV 64

Query: 116 IVLSWSGSSDELKAILYYARRFSIPLIAITSENKSVVACHADIVLTLPKEPESCPHGLAP 175
           I +S+SG + E       A+     +IAIT    S +A  ADIVL +  E        + 
Sbjct: 65  IAISFSGETKETVEAAEIAKERGAKVIAITDSANSPLAKLADIVLLVSSEEG--DFRSSA 122

Query: 176 TTSAIMQLAIGDALAIA 192
            +S I QLA+ DAL +A
Sbjct: 123 FSSRIAQLALIDALFLA 139


>gnl|CDD|32593 COG2524, COG2524, Predicted transcriptional regulator, contains
           C-terminal CBS domains [Transcription].
          Length = 294

 Score = 69.5 bits (170), Expect = 1e-12
 Identities = 34/106 (32%), Positives = 51/106 (48%), Gaps = 1/106 (0%)

Query: 232 LVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIK 291
            V+    L +A  +  EK      VVD+  K+ GIIT  DI +          V D M K
Sbjct: 184 TVRPDDTLREAAKLFYEKGIRGAPVVDDD-KIVGIITLSDIAKAIANGNLDAKVSDYMRK 242

Query: 292 NPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
           N   I ED  +  A++L+ ++N+  L+V D   K +GI+   D+L 
Sbjct: 243 NVITINEDEDIYDAIRLMNKNNVGRLLVTDSNGKPVGIITRTDILT 288



 Score = 27.5 bits (61), Expect = 5.5
 Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 284 SVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDL 335
            V+++M K    +  D  L  A +L  +  I    VVDD  K +GI+   D+
Sbjct: 173 KVKNLMSKKLITVRPDDTLREAAKLFYEKGIRGAPVVDD-DKIVGIITLSDI 223


>gnl|CDD|73111 cd04611, CBS_pair_PAS_GGDEF_DUF1_assoc, This cd contains two tandem
           repeats of the cystathionine beta-synthase (CBS pair)
           domains in association with a PAS domain, a GGDEF
           (DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain
           downstream. PAS domains have been found to bind ligands,
           and to act as sensors for light and oxygen in signal
           transduction. The GGDEF domain has been suggested to be
           homologous to the adenylyl cyclase catalytic domain and
           is thought to be involved in regulating cell surface
           adhesiveness in bacteria. CBS is a small domain
           originally identified in cystathionine beta-synthase and
           subsequently found in a wide range of different
           proteins. CBS domains usually come in tandem repeats,
           which associate to form a so-called Bateman domain or a
           CBS pair which is reflected in this model. The interface
           between the two CBS domains forms a cleft that is a
           potential ligand binding site. The CBS pair coexists
           with a variety of other functional domains.  It has been
           proposed that the CBS domain may play a regulatory role,
           although its exact function is unknown..
          Length = 111

 Score = 69.1 bits (169), Expect = 2e-12
 Identities = 38/110 (34%), Positives = 57/110 (51%), Gaps = 2/110 (1%)

Query: 229 SIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLN-TLSVED 287
            I        L +A + + E+R   + VVD+G+ L GI+TE DI R      +    V +
Sbjct: 2   QILTCPPDTSLAEAASRMRERRISSIVVVDDGRPL-GIVTERDILRLLASGPDLQTPVGE 60

Query: 288 VMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
           VM      +  DT L  A QL+R+H I  L+VVDD  + +G++   DLL+
Sbjct: 61  VMSSPLLTVPADTSLYDARQLMREHGIRHLVVVDDDGELLGLLSQTDLLQ 110



 Score = 35.2 bits (81), Expect = 0.024
 Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 6/60 (10%)

Query: 218 VCASDVMHSGDSIPLVKI--GCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRN 275
               +VM S    PL+ +     L DA  ++ E     + VVD+  +L G++++ D+ +N
Sbjct: 56  TPVGEVMSS----PLLTVPADTSLYDARQLMREHGIRHLVVVDDDGELLGLLSQTDLLQN 111


>gnl|CDD|73123 cd04624, CBS_pair_11, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 112

 Score = 68.3 bits (167), Expect = 3e-12
 Identities = 30/106 (28%), Positives = 57/106 (53%), Gaps = 1/106 (0%)

Query: 233 VKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLN-TLSVEDVMIK 291
           V     + +A  +++E+  G V VVD  ++  GI+TE DI R     ++    V ++M +
Sbjct: 6   VDPDTSIREAAKLMAEENVGSVVVVDPDERPIGIVTERDIVRAVAAGIDLDTPVSEIMTR 65

Query: 292 NPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
           +   +  D  +  A +L+R++NI   +VVD   + +G++   DL+R
Sbjct: 66  DLVTVDPDEPVAEAAKLMRKNNIRHHLVVDKGGELVGVISIRDLVR 111



 Score = 29.4 bits (66), Expect = 1.4
 Identities = 14/47 (29%), Positives = 27/47 (57%)

Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
           +    +  DT +  A +L+ + N+  ++VVD  ++ IGIV   D++R
Sbjct: 1   RPVVTVDPDTSIREAAKLMAEENVGSVVVVDPDERPIGIVTERDIVR 47


>gnl|CDD|30863 COG0517, COG0517, FOG: CBS domain [General function prediction
           only].
          Length = 117

 Score = 67.9 bits (165), Expect = 4e-12
 Identities = 43/112 (38%), Positives = 59/112 (52%), Gaps = 4/112 (3%)

Query: 228 DSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNF-HKDLNTLSVE 286
             +  VK    + DA+ ++SE     V VVD+G KL GIITE DI R         L V+
Sbjct: 7   KDVITVKPDTSVRDALLLMSENGVSAVPVVDDG-KLVGIITERDILRALAAGGKRLLPVK 65

Query: 287 DVMIKNPKVILEDTLLTVAMQLLRQ-HNISVLMVVDDCQ-KAIGIVHFLDLL 336
           +VM K    +  DT L  A++L+ + H I  L VVDD   K +GI+   D+L
Sbjct: 66  EVMTKPVVTVDPDTPLEEALELMVERHKIRRLPVVDDDGGKLVGIITLSDIL 117



 Score = 39.7 bits (92), Expect = 0.001
 Identities = 19/54 (35%), Positives = 33/54 (61%), Gaps = 1/54 (1%)

Query: 285 VEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
           V+D+M K+   +  DT +  A+ L+ ++ +S + VVDD  K +GI+   D+LR 
Sbjct: 1   VKDIMTKDVITVKPDTSVRDALLLMSENGVSAVPVVDD-GKLVGIITERDILRA 53


>gnl|CDD|73107 cd04607, CBS_pair_NTP_transferase_assoc, This cd contains two
           tandem repeats of the cystathionine beta-synthase (CBS
           pair) domain associated with the NTP (Nucleotidyl
           transferase) domain downstream.  CBS is a small domain
           originally identified in cystathionine beta-synthase and
           subsequently found in a wide range of different
           proteins. CBS domains usually come in tandem repeats,
           which associate to form a so-called Bateman domain or a
           CBS pair which is reflected in this model. The interface
           between the two CBS domains forms a cleft that is a
           potential ligand binding site. The CBS pair coexists
           with a variety of other functional domains.  It has been
           proposed that the CBS domain may play a regulatory role,
           although its exact function is unknown..
          Length = 113

 Score = 67.5 bits (165), Expect = 5e-12
 Identities = 31/107 (28%), Positives = 53/107 (49%), Gaps = 3/107 (2%)

Query: 232 LVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNF--HKDLNTLSVEDVM 289
           LV     ++DA+  + +     V VVDE  +L G +T+GDI R       L+   V +VM
Sbjct: 6   LVSPDASILDALRKIDKNALRIVLVVDENGRLLGTVTDGDIRRALLKGLSLDD-PVSEVM 64

Query: 290 IKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLL 336
            +NP      +     + L+R+ +I  L ++D+  + +G+    DLL
Sbjct: 65  NRNPITAKVGSSREEILALMRERSIRHLPILDEEGRVVGLATLDDLL 111


>gnl|CDD|73085 cd04585, CBS_pair_ACT_assoc2, This cd contains two tandem repeats
           of the cystathionine beta-synthase (CBS pair) domains in
            the acetoin utilization proteins in bacteria. Acetoin
           is a product of fermentative metabolism in many
           prokaryotic and eukaryotic microorganisms.  They produce
           acetoin as an external carbon storage compound and then
           later reuse it as a carbon and energy source during
           their stationary phase and sporulation. In addition
           these CBS domains are associated with a downstream ACT
           domain, which is linked to a wide range of metabolic
           enzymes that are regulated by amino acid concentration.
           Pairs of ACT domains bind specifically to a particular
           amino acid leading to regulation of the linked enzyme.
           CBS is a small domain originally identified in
           cystathionine beta-synthase and subsequently found in a
           wide range of different proteins. CBS domains usually
           come in tandem repeats, which associate to form a
           so-called Bateman domain or a CBS pair which is
           reflected in this model. The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains.  It has been proposed that the
           CBS domain may play a regulatory role, although its
           exact function is unknown..
          Length = 122

 Score = 66.4 bits (162), Expect = 1e-11
 Identities = 33/112 (29%), Positives = 56/112 (50%), Gaps = 13/112 (11%)

Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR------------NFHKDLNTLSV 285
            L++A+ ++ E     + VVD G KL GI+T+ D+                +  L+ + V
Sbjct: 11  SLMEALKLMKENSIRRLPVVDRG-KLVGIVTDRDLKLASPSKATTLDIWELYYLLSKIKV 69

Query: 286 EDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
            D+M ++P  +  D  +  A +L+ +  IS L VVDD  + +GI+   DL R
Sbjct: 70  SDIMTRDPITVSPDASVEEAAELMLERKISGLPVVDDQGRLVGIITESDLFR 121



 Score = 36.7 bits (85), Expect = 0.009
 Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 1/48 (2%)

Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
           KNP  +  DT L  A++L+++++I  L VVD   K +GIV   DL   
Sbjct: 1   KNPITVTPDTSLMEALKLMKENSIRRLPVVDR-GKLVGIVTDRDLKLA 47


>gnl|CDD|73101 cd04601, CBS_pair_IMPDH, This cd contains two tandem repeats of the
           cystathionine beta-synthase (CBS pair) domains in the
           inosine 5' monophosphate dehydrogenase (IMPDH) protein. 
           IMPDH is an essential enzyme that catalyzes the first
           step unique to GTP synthesis, playing a key role in the
           regulation of cell proliferation and differentiation.
           CBS is a small domain originally identified in
           cystathionine beta-synthase and subsequently found in a
           wide range of different proteins. CBS domains usually
           come in tandem repeats, which associate to form a
           so-called Bateman domain or a CBS pair which is
           reflected in this model. The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains. It has been proposed that the
           CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain in IMPDH have been
           associated with retinitis pigmentosa..
          Length = 110

 Score = 64.3 bits (157), Expect = 4e-11
 Identities = 32/101 (31%), Positives = 52/101 (51%), Gaps = 4/101 (3%)

Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVIL 297
            + +A+ +++E     + VVD+  KL GI+T  D+   F  DL+   V +VM     +  
Sbjct: 12  TVAEALELMAEYGISGLPVVDDDGKLVGIVTNRDL--RFETDLDK-PVSEVMTPENLLTT 68

Query: 298 E-DTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
              T L  A++LL +H I  L VVDD  K  G++   D+ +
Sbjct: 69  VEGTSLEEALELLHEHKIEKLPVVDDEGKLKGLITVKDIEK 109



 Score = 38.1 bits (89), Expect = 0.003
 Identities = 20/49 (40%), Positives = 30/49 (61%), Gaps = 1/49 (2%)

Query: 290 IKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
           I++P  +  D  +  A++L+ ++ IS L VVDD  K +GIV   D LRF
Sbjct: 1   IRDPITVSPDATVAEALELMAEYGISGLPVVDDDGKLVGIVTNRD-LRF 48



 Score = 34.7 bits (80), Expect = 0.043
 Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 220 ASDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI 272
            S+VM   + +     G  L +A+ +L E +   + VVD+  KLKG+IT  DI
Sbjct: 56  VSEVMTPENLL-TTVEGTSLEEALELLHEHKIEKLPVVDDEGKLKGLITVKDI 107


>gnl|CDD|73105 cd04605, CBS_pair_MET2_assoc, This cd contains two tandem repeats
           of the cystathionine beta-synthase (CBS pair) domains
           associated with the MET2 domain. Met2 is a key enzyme in
           the biosynthesis of methionine.  It encodes a homoserine
           transacetylase involved in converting homoserine to
           O-acetyl homoserine. CBS is a small domain originally
           identified in cystathionine beta-synthase and
           subsequently found in a wide range of different
           proteins. CBS domains usually come in tandem repeats,
           which associate to form a so-called Bateman domain or a
           CBS pair which is reflected in this model. The interface
           between the two CBS domains forms a cleft that is a
           potential ligand binding site. The CBS pair coexists
           with a variety of other functional domains. It has been
           proposed that the CBS domain may play a regulatory role,
           although its exact function is unknown..
          Length = 110

 Score = 64.1 bits (156), Expect = 5e-11
 Identities = 34/97 (35%), Positives = 53/97 (54%), Gaps = 2/97 (2%)

Query: 241 DAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILEDT 300
           +A  ++ E+    + VVDE  +L GI+T  DI +   +D    SVED+M +N      D 
Sbjct: 15  EAAKLMIEENINHLPVVDEDGRLVGIVTSWDISKAVARDKK--SVEDIMTRNVITATPDE 72

Query: 301 LLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
            + VA + + +HNIS L VVD   + IGI+   D+ +
Sbjct: 73  PIDVAARKMERHNISALPVVDAENRVIGIITSEDISK 109



 Score = 26.7 bits (59), Expect = 9.1
 Identities = 11/37 (29%), Positives = 17/37 (45%)

Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR 274
           P+  A   +       + VVD   ++ GIIT  DI +
Sbjct: 73  PIDVAARKMERHNISALPVVDAENRVIGIITSEDISK 109


>gnl|CDD|73087 cd04587, CBS_pair_CAP-ED_DUF294_PBI_assoc, This cd contains two
           tandem repeats of the cystathionine beta-synthase (CBS
           pair) domains associated with either the CAP_ED (cAMP
           receptor protein effector domain) family of
           transcription factors and the DUF294 domain or the PB1
           (Phox and Bem1p) domain.  Members of CAP_ED, include CAP
           which binds cAMP, FNR (fumarate and nitrate reductase)
           which uses an iron-sulfur cluster to sense oxygen, and
           CooA a heme containing CO sensor. In all cases binding
           of the effector leads to conformational changes and the
           ability to activate transcription. DUF294 is a putative
           nucleotidyltransferase with a conserved DxD motif. The
           PB1 domain adopts a beta-grasp fold, similar to that
           found in ubiquitin and Ras-binding domains. A motif,
           variously termed OPR, PC and AID, represents the most
           conserved region of the majority of PB1 domains, and is
           necessary for PB1 domain function. This function is the
           formation of PB1 domain heterodimers, although not all
           PB1 domain pairs associate. CBS is a small domain
           originally identified in cystathionine beta-synthase and
           subsequently found in a wide range of different
           proteins. CBS domains usually come in tandem repeats,
           which associate to form a so-called Bateman domain or a
           CBS pair which is reflected in this model. The interface
           between the two CBS domains forms a cleft that is a
           potential ligand binding site. The CBS pair coexists
           with a variety of other functional domains. It has been
           proposed that the CBS domain may play a regulatory role,
           although its exact function is unknown..
          Length = 113

 Score = 64.1 bits (156), Expect = 5e-11
 Identities = 35/111 (31%), Positives = 48/111 (43%), Gaps = 4/111 (3%)

Query: 228 DSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI-FRNF--HKDLNTLS 284
                V     + +A  ++ EKR  CV V+D   KL GI T  DI  R      D  +  
Sbjct: 1   TKPATVSPTTTVQEAAKLMREKRVSCVLVMDGN-KLVGIFTSKDIALRVVAQGLDPESTL 59

Query: 285 VEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDL 335
           VE VM  NP     DT +  A+ L+ Q     L VVD   + +G++    L
Sbjct: 60  VERVMTPNPVCATSDTPVLEALHLMVQGKFRHLPVVDKSGQVVGLLDVTKL 110



 Score = 26.7 bits (59), Expect = 9.2
 Identities = 7/38 (18%), Positives = 22/38 (57%)

Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRN 275
           P+++A+ ++ + +F  + VVD+  ++ G++    +   
Sbjct: 76  PVLEALHLMVQGKFRHLPVVDKSGQVVGLLDVTKLTHA 113


>gnl|CDD|73121 cd04622, CBS_pair_9, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 113

 Score = 64.0 bits (156), Expect = 6e-11
 Identities = 34/104 (32%), Positives = 55/104 (52%), Gaps = 4/104 (3%)

Query: 237 CPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI-FRNF--HKDLNTLSVEDVMIKNP 293
             + +A  ++ E   G + V +   +L GI+T+ DI  R     +D +T +V DVM +  
Sbjct: 10  DTIREAARLMREHDVGALPVCEND-RLVGIVTDRDIVVRAVAEGRDPDTTTVGDVMTRGV 68

Query: 294 KVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
             + ED  +  A +L+R+H +  L VVDD  + +GIV   DL R
Sbjct: 69  VTVTEDDDVDEAARLMREHQVRRLPVVDDDGRLVGIVSLGDLAR 112



 Score = 27.8 bits (62), Expect = 4.7
 Identities = 10/40 (25%), Positives = 23/40 (57%), Gaps = 1/40 (2%)

Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIV 330
           ++   +  D  +  A +L+R+H++  L V ++  + +GIV
Sbjct: 1   RDVVTVSPDDTIREAARLMREHDVGALPVCEN-DRLVGIV 39


>gnl|CDD|73088 cd04588, CBS_pair_CAP-ED_DUF294_assoc_arch, This cd contains two
           tandem repeats of the cystathionine beta-synthase (CBS
           pair) domains associated with the archaeal CAP_ED (cAMP
           receptor protein effector domain) family of
           transcription factors and the DUF294 domain.  Members of
           CAP_ED, include CAP which binds cAMP, FNR (fumarate and
           nitrate reductase) which uses an iron-sulfur cluster to
           sense oxygen, and CooA a heme containing CO sensor. In
           all cases binding of the effector leads to
           conformational changes and the ability to activate
           transcription. DUF294 is a putative
           nucleotidyltransferase with a conserved DxD motif. CBS
           is a small domain originally identified in cystathionine
           beta-synthase and subsequently found in a wide range of
           different proteins. CBS domains usually come in tandem
           repeats, which associate to form a so-called Bateman
           domain or a CBS pair which is reflected in this model.
           The interface between the two CBS domains forms a cleft
           that is a potential ligand binding site. The CBS pair
           coexists with a variety of other functional domains. It
           has been proposed that the CBS domain may play a
           regulatory role, although its exact function is
           unknown..
          Length = 110

 Score = 62.1 bits (151), Expect = 2e-10
 Identities = 36/106 (33%), Positives = 55/106 (51%), Gaps = 1/106 (0%)

Query: 232 LVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIK 291
            +     L +A  + +        VVD+G KL GI+T  DI     + L    V+DVM K
Sbjct: 5   TLNPNATLREAARLFNTHHIHGAPVVDDG-KLVGIVTLSDIAHAIARGLELAKVKDVMTK 63

Query: 292 NPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
           +   I ED  L  A++L+ +HN+  L+V DD  + +GI+   D+LR
Sbjct: 64  DVITIDEDEQLYDAIRLMNKHNVGRLIVTDDEGRPVGIITRTDILR 109


>gnl|CDD|73135 cd04637, CBS_pair_24, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 122

 Score = 60.3 bits (146), Expect = 8e-10
 Identities = 33/112 (29%), Positives = 60/112 (53%), Gaps = 13/112 (11%)

Query: 239 LIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNF----------HKDLNTLS--VE 286
           L +   I  + +F  + VV++ + L G+I++ D  +             KDL TL+    
Sbjct: 12  LEEVREIFEKHKFHHLLVVEDNE-LVGVISDRDYLKAISPFLGTAGETEKDLATLNRRAH 70

Query: 287 DVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
            +M ++P  +  DT +  A +LL +++IS L VVD+  + IGI+ + DLL++
Sbjct: 71  QIMTRDPITVSPDTPVDEASKLLLENSISCLPVVDENGQLIGIITWKDLLKY 122



 Score = 39.1 bits (91), Expect = 0.002
 Identities = 23/62 (37%), Positives = 32/62 (51%), Gaps = 2/62 (3%)

Query: 213 LGTLFVCASDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI 272
           L TL   A  +M + D I  V    P+ +A  +L E    C+ VVDE  +L GIIT  D+
Sbjct: 62  LATLNRRAHQIM-TRDPI-TVSPDTPVDEASKLLLENSISCLPVVDENGQLIGIITWKDL 119

Query: 273 FR 274
            +
Sbjct: 120 LK 121


>gnl|CDD|73119 cd04620, CBS_pair_7, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 115

 Score = 60.2 bits (146), Expect = 9e-10
 Identities = 36/104 (34%), Positives = 54/104 (51%), Gaps = 4/104 (3%)

Query: 231 PLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR--NFHKDLNTLSVEDV 288
             V    P+ DAI ++S++      +V E  +L GI TE DI R     KDL+ L + +V
Sbjct: 4   LTVTPDTPVADAIALMSQQGDSSCVLVVEKGRLLGIFTERDIVRLTAIGKDLSDLPIGEV 63

Query: 289 MIKNPKVILEDTLLTV--AMQLLRQHNISVLMVVDDCQKAIGIV 330
           M +    + E  +  +  A+ L RQH I  L V+DD  + IG+V
Sbjct: 64  MTQPVVTLQESEIQDIFTALSLFRQHQIRHLPVLDDQGQLIGLV 107


>gnl|CDD|73129 cd04631, CBS_pair_18, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 125

 Score = 59.8 bits (145), Expect = 9e-10
 Identities = 37/120 (30%), Positives = 52/120 (43%), Gaps = 14/120 (11%)

Query: 233 VKIGCPLIDAITILSEKRFGCVAVVDEGQ-KLKGIITEGDIFRNFHKDLNTLS------- 284
           V    P+++A  I+    F  + VVDEG  KL GIIT  DI +                 
Sbjct: 6   VPPTTPIMEAAKIMVRNGFRRLPVVDEGTGKLVGIITATDILKYLGGGEKFNKIKTGNGL 65

Query: 285 ------VEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
                 V  +M +N   I  D  +  A +L+ +  +  L VVDD  K +GIV   DLL+ 
Sbjct: 66  EAINEPVRSIMTRNVITITPDDSIKDAAELMLEKRVGGLPVVDDDGKLVGIVTERDLLKA 125


>gnl|CDD|73086 cd04586, CBS_pair_BON_assoc, This cd contains two tandem repeats of
           the cystathionine beta-synthase (CBS pair) domains
           associated with the BON (bacterial OsmY and nodulation
           domain) domain. BON is a putative phospholipid-binding
           domain found in a family of osmotic shock protection
           proteins. It is also found in some secretins and a group
           of potential haemolysins. Its likely function is
           attachment to phospholipid membranes. CBS is a small
           domain originally identified in cystathionine
           beta-synthase and subsequently found in a wide range of
           different proteins. CBS domains usually come in tandem
           repeats, which associate to form a so-called Bateman
           domain or a CBS pair which is reflected in this model.
           The interface between the two CBS domains forms a cleft
           that is a potential ligand binding site. The CBS pair
           coexists with a variety of other functional domains. It
           has been proposed that the CBS domain may play a
           regulatory role, although its exact function is
           unknown..
          Length = 135

 Score = 59.4 bits (144), Expect = 1e-09
 Identities = 32/133 (24%), Positives = 54/133 (40%), Gaps = 27/133 (20%)

Query: 231 PLVKIG--CPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNF------------ 276
            +V +     + +A  ++ +     + VVD+  +L GI++EGD+ R              
Sbjct: 3   DVVTVSPETSVAEAARLMLDNHISGLPVVDDDGRLVGIVSEGDLLRRAELGTERRRARWL 62

Query: 277 ------------HKDLNTLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQ 324
                           +   V DVM +    + EDT L    +L+ +H I  + VV    
Sbjct: 63  DLLAGAEELAAAFVRSHGRKVADVMTRPVVTVGEDTPLAEVAELMEEHRIKRVPVVRG-G 121

Query: 325 KAIGIVHFLDLLR 337
           + +GIV   DLLR
Sbjct: 122 RLVGIVSRADLLR 134


>gnl|CDD|88405 cd05008, SIS_GlmS_GlmD_1, SIS (Sugar ISomerase) domain repeat 1
           found in Glucosamine 6-phosphate synthase (GlmS) and
           Glucosamine-6-phosphate deaminase (GlmD). The SIS domain
           is found in many phosphosugar isomerases and
           phosphosugar binding proteins. GlmS contains a
           N-terminal glutaminase domain and two C-terminal SIS
           domains and catalyzes the first step in hexosamine
           metabolism, converting fructose 6-phosphate into
           glucosamine 6-phosphate using glutamine as nitrogen
           source. The glutaminase domain hydrolyzes glutamine to
           glutamate and ammonia. Ammonia is transferred through a
           channel to the isomerase domain for glucosamine
           6-phosphate synthesis. The end product of the pathway is
           N-acetylglucosamine, which plays multiple roles in
           eukaryotic cells including being a building block of
           bacterial and fungal cell walls. In the absence of
           glutamine, GlmS catalyzes the isomerization of fructose
           6-phosphate into glucose 6- phosphate (PGI-like
           activity). Glucosamine-6-phosphate deaminase (GlmD)
           contains two SIS domains and catalyzes the deamination
           and isomerization of glucosamine-6-phosphate into
           fructose-6-phosphate with the release of ammonia; in
           presence of high ammonia concentration, GlmD can
           catalyze the reverse reaction..
          Length = 126

 Score = 58.6 bits (142), Expect = 2e-09
 Identities = 39/128 (30%), Positives = 54/128 (42%), Gaps = 3/128 (2%)

Query: 66  RVVITGIGKSGHIGSKLASTLASTGTPSFFVHAAEASHGDLGMITRDDLIIVLSWSGSSD 125
           R++I G G S H        L         V AA        ++  D L+I +S SG + 
Sbjct: 1   RILIVGCGTSYHAALVAKYLLERLAGIPVEVEAASEFRYRRPLLDEDTLVIAISQSGETA 60

Query: 126 ELKAILYYARRFSIPLIAITSENKSVVACHADIVLTLPKEPESCPHGLAPTTSAIMQLAI 185
           +  A L  A+      +AIT+   S +A  AD VL L   PE     +A T +   QL  
Sbjct: 61  DTLAALRLAKEKGAKTVAITNVVGSTLAREADYVLYLRAGPE---ISVAATKAFTSQLLA 117

Query: 186 GDALAIAL 193
              LA+AL
Sbjct: 118 LLLLALAL 125


>gnl|CDD|73084 cd04584, CBS_pair_ACT_assoc, This cd contains two tandem repeats of
           the cystathionine beta-synthase (CBS pair) domains in
           the acetoin utilization proteins in bacteria. Acetoin is
           a product of fermentative metabolism in many prokaryotic
           and eukaryotic microorganisms.  They produce acetoin as
           an external carbon storage compound and then later reuse
           it as a carbon and energy source during their stationary
           phase and sporulation. In addition these CBS domains are
           associated with a downstream ACT domain, which is linked
           to a wide range of metabolic enzymes that are regulated
           by amino acid concentration. Pairs of ACT domains bind
           specifically to a particular amino acid leading to
           regulation of the linked enzyme. CBS is a small domain
           originally identified in cystathionine beta-synthase and
           subsequently found in a wide range of different
           proteins. CBS domains usually come in tandem repeats,
           which associate to form a so-called Bateman domain or a
           CBS pair which is reflected in this model. The interface
           between the two CBS domains forms a cleft that is a
           potential ligand binding site. The CBS pair coexists
           with a variety of other functional domains.  It has been
           proposed that the CBS domain may play a regulatory role,
           although its exact function is unknown..
          Length = 121

 Score = 58.3 bits (141), Expect = 3e-09
 Identities = 32/110 (29%), Positives = 55/110 (50%), Gaps = 12/110 (10%)

Query: 239 LIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLS-----------VED 287
           + +A+ ++ E +   + VVDE  +L GI+T+ D+         TLS           V++
Sbjct: 12  IAEALELMREHKIRHLPVVDEEGRLVGIVTDRDLRDASPSPFTTLSEHELYLLLKMPVKE 71

Query: 288 VMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
           +M K+   +     +  A  L+R+H I  L VV+D  + +GI+   DLLR
Sbjct: 72  IMTKDVITVHPLDTVEEAALLMREHRIGCLPVVED-GRLVGIITETDLLR 120



 Score = 39.4 bits (92), Expect = 0.002
 Identities = 16/37 (43%), Positives = 25/37 (67%), Gaps = 1/37 (2%)

Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR 274
            + +A  ++ E R GC+ VV++G +L GIITE D+ R
Sbjct: 85  TVEEAALLMREHRIGCLPVVEDG-RLVGIITETDLLR 120



 Score = 31.3 bits (71), Expect = 0.39
 Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 1/40 (2%)

Query: 298 EDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
             T+   A++L+R+H I  L VVD+  + +GIV   DL  
Sbjct: 9   TTTIAE-ALELMREHKIRHLPVVDEEGRLVGIVTDRDLRD 47


>gnl|CDD|73142 cd04800, CBS_pair_CAP-ED_DUF294_PBI_assoc2, This cd contains two
           tandem repeats of the cystathionine beta-synthase (CBS
           pair) domains associated with either the CAP_ED (cAMP
           receptor protein effector domain) family of
           transcription factors and the DUF294 domain or the PB1
           (Phox and Bem1p) domain.  Members of CAP_ED, include CAP
           which binds cAMP, FNR (fumarate and nitrate reductase)
           which uses an iron-sulfur cluster to sense oxygen, and
           CooA a heme containing CO sensor. In all cases binding
           of the effector leads to conformational changes and the
           ability to activate transcription. DUF294 is a putative
           nucleotidyltransferase with a conserved DxD motif. The
           PB1 domain adopts a beta-grasp fold, similar to that
           found in ubiquitin and Ras-binding domains. A motif,
           variously termed OPR, PC and AID, represents the most
           conserved region of the majority of PB1 domains, and is
           necessary for PB1 domain function. This function is the
           formation of PB1 domain heterodimers, although not all
           PB1 domain pairs associate. CBS is a small domain
           originally identified in cystathionine beta-synthase and
           subsequently found in a wide range of different
           proteins. CBS domains usually come in tandem repeats,
           which associate to form a so-called Bateman domain or a
           CBS pair which is reflected in this model. The interface
           between the two CBS domains forms a cleft that is a
           potential ligand binding site. The CBS pair coexists
           with a variety of other functional domains. It has been
           proposed that the CBS domain may play a regulatory role,
           although its exact function is unknown..
          Length = 111

 Score = 58.2 bits (141), Expect = 3e-09
 Identities = 33/103 (32%), Positives = 55/103 (53%), Gaps = 4/103 (3%)

Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI-FRNFHKDLN-TLSVEDVMIKNPKV 295
            + +A  +++E R   + VVD+G +L GI+T+ D+  R   + L+    V +VM   P  
Sbjct: 11  TIREAARLMTEHRVSSLLVVDDG-RLVGIVTDRDLRNRVVAEGLDPDTPVSEVMTAPPIT 69

Query: 296 ILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
           I  D  +  A+ L+ +  I  L VVDD  + +G++   DLLR 
Sbjct: 70  IPPDATVFEALLLMLERGIHHLPVVDD-GRLVGVISATDLLRL 111


>gnl|CDD|73115 cd04615, CBS_pair_2, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 113

 Score = 58.0 bits (140), Expect = 4e-09
 Identities = 32/107 (29%), Positives = 50/107 (46%), Gaps = 2/107 (1%)

Query: 233 VKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNF--HKDLNTLSVEDVMI 290
           V +   +  A+  +       + VVD+ ++L GIIT  D+       ++L    V +VM 
Sbjct: 6   VVLNTDIARAVAEMYTSGSRALPVVDDKKRLVGIITRYDVLSYALESEELKDAKVREVMN 65

Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
                I  +  +  A  L+  +NIS L V+DD  K  GIV   D+LR
Sbjct: 66  SPVITIDANDSIAKARWLMSNNNISRLPVLDDKGKVGGIVTEDDILR 112


>gnl|CDD|73136 cd04638, CBS_pair_25, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 106

 Score = 56.8 bits (137), Expect = 8e-09
 Identities = 32/97 (32%), Positives = 53/97 (54%), Gaps = 5/97 (5%)

Query: 241 DAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILEDT 300
           D + +L E +   V VV +  +L GIIT  D+ RN  ++   L    +M ++P  +  D 
Sbjct: 14  DVLELLKEYKVSGVPVVKKSGELVGIITRKDLLRNPEEEQLAL----LMTRDPPTVSPDD 69

Query: 301 LLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
            +  A +L+ ++NI  + VVDD  K +GIV   D++R
Sbjct: 70  DVKEAAKLMVENNIRRVPVVDD-GKLVGIVTVADIVR 105


>gnl|CDD|73083 cd04583, CBS_pair_ABC_OpuCA_assoc2, This cd contains two tandem
           repeats of the cystathionine beta-synthase (CBS pair)
           domains in association with the ABC transporter OpuCA.
           OpuCA is the ATP binding component of a bacterial solute
           transporter that serves a protective role to cells
           growing in a hyperosmolar environment but the function
           of the CBS domains in OpuCA remains unknown.  In the
           related ABC transporter, OpuA, the tandem CBS domains
           have been shown to function as sensors for ionic
           strength, whereby they control the transport activity
           through an electronic switching mechanism. ABC
           transporters are a large family of proteins involved in
           the transport of a wide variety of different compounds,
           like sugars, ions, peptides, and more complex organic
           molecules. They are a subset of nucleotide hydrolases
           that contain a signature motif, Q-loop, and
           H-loop/switch region, in addition to the Walker A
           motif/P-loop and Walker B motif commonly found in a
           number of ATP- and GTP-binding and hydrolyzing proteins.
           CBS is a small domain originally identified in
           cystathionine beta-synthase and subsequently found in a
           wide range of different proteins. CBS domains usually
           come in tandem repeats, which associate to form a
           so-called Bateman domain or a CBS pair which is
           reflected in this model. The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains.  It has been proposed that the
           CBS domain may play a regulatory role, although its
           exact function is unknown..
          Length = 109

 Score = 55.6 bits (134), Expect = 2e-08
 Identities = 23/92 (25%), Positives = 50/92 (54%), Gaps = 3/92 (3%)

Query: 239 LIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILE 298
           L +AI ++ +K+   + VVD+  KL GI++   + + + +     S+ED+M+++   +  
Sbjct: 13  LAEAIKLMRDKKVDSLLVVDKDNKLLGIVSLESLEQAYKEAK---SLEDIMLEDVFTVQP 69

Query: 299 DTLLTVAMQLLRQHNISVLMVVDDCQKAIGIV 330
           D  L   + L+ +     + VVD+  K +G++
Sbjct: 70  DASLRDVLGLVLKRGPKYVPVVDEDGKLVGLI 101



 Score = 34.4 bits (79), Expect = 0.043
 Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 2/51 (3%)

Query: 220 ASDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEG 270
             D+M     +  V+    L D + ++ ++    V VVDE  KL G+IT  
Sbjct: 56  LEDIMLE--DVFTVQPDASLRDVLGLVLKRGPKYVPVVDEDGKLVGLITRS 104



 Score = 33.2 bits (76), Expect = 0.10
 Identities = 18/41 (43%), Positives = 24/41 (58%)

Query: 290 IKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIV 330
           IKNP  I  D  L  A++L+R   +  L+VVD   K +GIV
Sbjct: 1   IKNPVTITPDRTLAEAIKLMRDKKVDSLLVVDKDNKLLGIV 41


>gnl|CDD|73095 cd04595, CBS_pair_DHH_polyA_Pol_assoc, This cd contains two tandem
           repeats of the cystathionine beta-synthase (CBS pair)
           domains associated with an upstream DHH domain which
           performs a phosphoesterase function and a downstream
           polyA polymerase domain. CBS is a small domain
           originally identified in cystathionine beta-synthase and
           subsequently found in a wide range of different
           proteins. CBS domains usually come in tandem repeats,
           which associate to form a so-called Bateman domain or a
           CBS pair which is reflected in this model. The interface
           between the two CBS domains forms a cleft that is a
           potential ligand binding site. The CBS pair coexists
           with a variety of other functional domains. It has been
           proposed that the CBS domain may play a regulatory role,
           although its exact function is unknown..
          Length = 110

 Score = 54.8 bits (132), Expect = 4e-08
 Identities = 30/90 (33%), Positives = 49/90 (54%), Gaps = 2/90 (2%)

Query: 250 RFGCVAV-VDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILEDTLLTVAMQL 308
           R+G  A+ V EG ++ GII+  D+ +     L    V+D M  +   +  DT L+   +L
Sbjct: 22  RYGHTALPVVEGGRVVGIISRRDVEKALRHGLGHAPVKDYMSTDVVTVPPDTPLSEVQEL 81

Query: 309 LRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
           + +H+I  + VV+D  + +GIV   DLLR 
Sbjct: 82  MVEHDIGRVPVVED-GRLVGIVTRTDLLRT 110


>gnl|CDD|73113 cd04613, CBS_pair_SpoIVFB_EriC_assoc2, This cd contains two tandem
           repeats of the cystathionine beta-synthase (CBS pair)
           domains in association with either the SpoIVFB domain
           (sporulation protein, stage IV cell wall formation, F
           locus, promoter-distal B) or the chloride channel
           protein EriC.  SpoIVFB is one of 4 proteins involved in
           endospore formation; the others are SpoIVFA (sporulation
           protein, stage IV cell wall formation, F locus,
           promoter-proximal A), BofA (bypass-of-forespore A ), and
           SpoIVB (sporulation protein, stage IV cell wall
           formation, B locus).  SpoIVFB is negatively regulated by
           SpoIVFA and BofA and activated by SpoIVB.  It is thought
           that SpoIVFB, SpoIVFA, and BofA are located in the
           mother-cell membrane that surrounds the forespore and
           that SpoIVB is secreted from the forespore into the
           space between the two where it activates SpoIVFB. EriC
           is involved in inorganic ion transport and metabolism.
           CBS is a small domain originally identified in
           cystathionine beta-synthase and subsequently found in a
           wide range of different proteins. CBS domains usually
           come in tandem repeats, which associate to form a
           so-called Bateman domain or a CBS pair which is
           reflected in this model. The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains.  It has been proposed that the
           CBS domain may play a regulatory role, although its
           exact function is unknown..
          Length = 114

 Score = 54.8 bits (132), Expect = 4e-08
 Identities = 28/102 (27%), Positives = 47/102 (46%), Gaps = 3/102 (2%)

Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKD--LNTLSVEDVMIKNPKV 295
           PL + + +++        VVD+  +L GI++  DI          + +   D+M K P V
Sbjct: 11  PLNELLDVIAHSPENNFPVVDDDGRLVGIVSLDDIREILFDPSLYDLVVASDIMTKPPVV 70

Query: 296 ILEDTLLTVAMQLLRQHNISVLMVVDDCQ-KAIGIVHFLDLL 336
           +  +  L  A++     +   L VVDD   K +GI+   DLL
Sbjct: 71  VYPEDSLEDALKKFEDSDYEQLPVVDDDPGKLLGILSRSDLL 112



 Score = 29.3 bits (66), Expect = 1.6
 Identities = 13/48 (27%), Positives = 22/48 (45%)

Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
           ++   I EDT L   + ++     +   VVDD  + +GIV   D+   
Sbjct: 1   RDVVTIPEDTPLNELLDVIAHSPENNFPVVDDDGRLVGIVSLDDIREI 48


>gnl|CDD|73112 cd04612, CBS_pair_SpoIVFB_EriC_assoc, This cd contains two tandem
           repeats of the cystathionine beta-synthase (CBS pair)
           domains in association with either the SpoIVFB domain
           (sporulation protein, stage IV cell wall formation, F
           locus, promoter-distal B) or the chloride channel
           protein EriC.  SpoIVFB is one of 4 proteins involved in
           endospore formation; the others are SpoIVFA (sporulation
           protein, stage IV cell wall formation, F locus,
           promoter-proximal A), BofA (bypass-of-forespore A ), and
           SpoIVB (sporulation protein, stage IV cell wall
           formation, B locus).  SpoIVFB is negatively regulated by
           SpoIVFA and BofA and activated by SpoIVB.  It is thought
           that SpoIVFB, SpoIVFA, and BofA are located in the
           mother-cell membrane that surrounds the forespore and
           that SpoIVB is secreted from the forespore into the
           space between the two where it activates SpoIVFB. EriC
           is involved in inorganic ion transport and metabolism.
           CBS is a small domain originally identified in
           cystathionine beta-synthase and subsequently found in a
           wide range of different proteins. CBS domains usually
           come in tandem repeats, which associate to form a
           so-called Bateman domain or a CBS pair which is
           reflected in this model. The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains.  It has been proposed that the
           CBS domain may play a regulatory role, although its
           exact function is unknown..
          Length = 111

 Score = 54.5 bits (131), Expect = 4e-08
 Identities = 34/102 (33%), Positives = 53/102 (51%), Gaps = 2/102 (1%)

Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR-NFHKDLNTLSVEDVMIKNPKVI 296
            + + + ++  +R     VVD+G +L GI+T  DI R        T+ V DVM ++P   
Sbjct: 11  TVDEVLALMFGERHRGYPVVDDG-RLVGIVTLADIRRVPAEGREATVLVGDVMTRDPVTA 69

Query: 297 LEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
             D  L  A++ + + +I  L VVDD  + +GIV   DLLR 
Sbjct: 70  SPDETLRDALKRMAERDIGRLPVVDDSGRLVGIVSRSDLLRA 111



 Score = 37.9 bits (88), Expect = 0.004
 Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 2/55 (3%)

Query: 220 ASDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR 274
             DVM              L DA+  ++E+  G + VVD+  +L GI++  D+ R
Sbjct: 58  VGDVMT--RDPVTASPDETLRDALKRMAERDIGRLPVVDDSGRLVGIVSRSDLLR 110


>gnl|CDD|144238 pfam00571, CBS, CBS domain.  CBS domains are small intracellular
           modules that pair together to form a stable globular
           domain. This family represents a single CBS domain.
           Pairs of these domains have been termed a Bateman
           domain. CBS domains have been shown to bind ligands with
           an adenosyl group such as AMP, ATP and S-AdoMet. CBS
           domains are found attached to a wide range of other
           protein domains suggesting that CBS domains may play a
           regulatory role making proteins sensitive to adenosyl
           carrying ligands. The region containing the CBS domains
           in Cystathionine-beta synthase is involved in regulation
           by S-AdoMet. CBS domain pairs from AMPK bind AMP or ATP.
           The CBS domains from IMPDH and the chloride channel CLC2
           bind ATP.
          Length = 57

 Score = 54.5 bits (132), Expect = 4e-08
 Identities = 23/54 (42%), Positives = 34/54 (62%)

Query: 285 VEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
           V+D+M  +   +  DT L  A++L+R++ IS L VVD+  K +GIV   DLLR 
Sbjct: 1   VKDIMTPDVVTVPPDTSLEEALELMRENGISRLPVVDEDGKLVGIVTLRDLLRA 54



 Score = 49.9 bits (120), Expect = 1e-06
 Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 2/59 (3%)

Query: 220 ASDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHK 278
             D+M     +  V     L +A+ ++ E     + VVDE  KL GI+T  D+ R    
Sbjct: 1   VKDIMTP--DVVTVPPDTSLEEALELMRENGISRLPVVDEDGKLVGIVTLRDLLRALLG 57


>gnl|CDD|144171 pfam00478, IMPDH, IMP dehydrogenase / GMP reductase domain.  This
           family is involved in biosynthesis of guanosine
           nucleotide. Members of this family contain a TIM barrel
           structure. In the inosine monophosphate dehydrogenases 2
           CBS domains pfam00571 are inserted in the TIM barrel.
           This family is a member of the common phosphate binding
           site TIM barrel family.
          Length = 467

 Score = 54.2 bits (131), Expect = 6e-08
 Identities = 22/100 (22%), Positives = 45/100 (45%), Gaps = 2/100 (2%)

Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVIL 297
            + +A+ +        V V ++G+ L G++            L+ +SV   M ++     
Sbjct: 100 TVAEALELKERYGISGVPVTEDGKLLGGLVGIRT--SRDIDFLSKVSVVMTMTEDLVTAP 157

Query: 298 EDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
           E   L  A ++L +H I  L +VDD  + +G++   D+ +
Sbjct: 158 EGITLEEANEILHEHKIEKLPIVDDDGELVGLITRKDIEK 197



 Score = 34.2 bits (79), Expect = 0.049
 Identities = 17/55 (30%), Positives = 27/55 (49%)

Query: 221 SDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRN 275
           S VM   + +     G  L +A  IL E +   + +VD+  +L G+IT  DI + 
Sbjct: 144 SVVMTMTEDLVTAPEGITLEEANEILHEHKIEKLPIVDDDGELVGLITRKDIEKA 198


>gnl|CDD|73145 cd04803, CBS_pair_15, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 122

 Score = 52.9 bits (127), Expect = 1e-07
 Identities = 32/112 (28%), Positives = 51/112 (45%), Gaps = 11/112 (9%)

Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR-----------NFHKDLNTLSVE 286
            L DA  ++ E R   + VV+E  KL G++T+ D+ R                   + V 
Sbjct: 11  SLADAEELMREHRIRHLPVVNEDGKLVGLLTQRDLLRAALSSLSDNGEESLTKERDVPVA 70

Query: 287 DVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
           +VM  +   +  DT L  A +++ ++ I  L VVDD    +GI+   D LR 
Sbjct: 71  EVMKTDVLTVTPDTPLREAAEIMVENKIGCLPVVDDKGTLVGIITRSDFLRL 122



 Score = 47.1 bits (112), Expect = 6e-06
 Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 2/54 (3%)

Query: 221 SDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR 274
           ++VM +   +  V    PL +A  I+ E + GC+ VVD+   L GIIT  D  R
Sbjct: 70  AEVMKT--DVLTVTPDTPLREAAEIMVENKIGCLPVVDDKGTLVGIITRSDFLR 121



 Score = 33.3 bits (76), Expect = 0.10
 Identities = 17/50 (34%), Positives = 27/50 (54%)

Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRFGI 340
                + ED  L  A +L+R+H I  L VV++  K +G++   DLLR  +
Sbjct: 1   SPVVTLSEDDSLADAEELMREHRIRHLPVVNEDGKLVGLLTQRDLLRAAL 50


>gnl|CDD|88402 cd05005, SIS_PHI, Hexulose-6-phosphate isomerase (PHI). PHI is a
           member of the SIS (Sugar ISomerase domain) superfamily.
           In the ribulose monophosphate pathway of formaldehyde
           fixation, hexulose-6-phosphate synthase catalyzes the
           condensation of ribulose-5-phosphate with formadelhyde
           to become hexulose-6-phosphate, which is then isomerized
           to fructose-6-phosphate by PHI..
          Length = 179

 Score = 52.9 bits (127), Expect = 1e-07
 Identities = 38/163 (23%), Positives = 63/163 (38%), Gaps = 12/163 (7%)

Query: 52  QFHCAVEKIKAIKGRVVITGIGKSGHIGSKLASTLASTGTPSFFVHAAEASHGDLGMITR 111
           +    +  I   K R+ + G G+SG +    A  L   G   + V            I  
Sbjct: 22  ELDKLISAILNAK-RIFVYGAGRSGLVAKAFAMRLMHLGLNVYVVGETTTPA-----IGP 75

Query: 112 DDLIIVLSWSGSSDELKAILYYARRFSIPLIAITSENKSVVACHADIVLTLP----KEPE 167
            DL+I +S SG +  +      A++    ++ ITS   S +A  AD+V+ +P     +  
Sbjct: 76  GDLLIAISGSGETSSVVNAAEKAKKAGAKVVLITSNPDSPLAKLADVVVVIPAATKDDHG 135

Query: 168 SCPHGLAPTTSAIMQLA--IGDALAIALLESRNFSENDFYVLH 208
                + P  +   Q A    DA+   L+E    SE +    H
Sbjct: 136 GEHKSIQPLGTLFEQSALVFLDAVIAKLMEELGVSEEEMKKRH 178


>gnl|CDD|73141 cd04643, CBS_pair_30, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 116

 Score = 52.9 bits (127), Expect = 1e-07
 Identities = 31/105 (29%), Positives = 48/105 (45%), Gaps = 9/105 (8%)

Query: 233 VKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI------FRNFH-KDLNTLSV 285
           V+    L  A+ +L++  +  + V+D+  K  G I+  DI        N   + L  L V
Sbjct: 6   VQDTNTLRHALLVLTKHGYSAIPVLDKEGKYVGTISLTDILWKLKGLENLDLERLVDLKV 65

Query: 286 EDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIV 330
            DVM  +  VI++D  +   + LL       L VVDD    IGI+
Sbjct: 66  IDVMNTDVPVIIDDADIEEILHLLIDQPF--LPVVDDDGIFIGII 108


>gnl|CDD|73099 cd04599, CBS_pair_GGDEF_assoc2, This cd contains two tandem repeats
           of the cystathionine beta-synthase (CBS pair) domains in
           association with the GGDEF (DiGuanylate-Cyclase (DGC))
           domain. The GGDEF domain has been suggested to be
           homologous to the adenylyl cyclase catalytic domain and
           is thought to be involved in regulating cell surface
           adhesiveness in bacteria. CBS is a small domain
           originally identified in cystathionine beta-synthase and
           subsequently found in a wide range of different
           proteins. CBS domains usually come in tandem repeats,
           which associate to form a so-called Bateman domain or a
           CBS pair which is reflected in this model. The interface
           between the two CBS domains forms a cleft that is a
           potential ligand binding site. The CBS pair coexists
           with a variety of other functional domains. It has been
           proposed that the CBS domain may play a regulatory role,
           although its exact function is unknown..
          Length = 105

 Score = 52.2 bits (125), Expect = 2e-07
 Identities = 30/97 (30%), Positives = 47/97 (48%), Gaps = 6/97 (6%)

Query: 241 DAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILEDT 300
            A  ++ + R G + VV++G KL GIIT  D+ R  H   N L V D M +    I  + 
Sbjct: 14  RAARLMEKHRIGGLPVVEDG-KLVGIITSRDV-RRAHP--NRL-VADAMTREVVTISPEA 68

Query: 301 LLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
            L  A +L+ +  I  L V+ +  K +GI+    +  
Sbjct: 69  SLLEAKRLMEEKKIERLPVLRER-KLVGIITKGTIAL 104


>gnl|CDD|73134 cd04636, CBS_pair_23, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 132

 Score = 51.4 bits (123), Expect = 3e-07
 Identities = 35/122 (28%), Positives = 55/122 (45%), Gaps = 23/122 (18%)

Query: 239 LIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHK-------------------- 278
           L D + IL   +   V VVD   ++ GI++EGD+ R  +K                    
Sbjct: 12  LRDVVEILLTGKISGVPVVDNEGRVVGIVSEGDLIRKIYKGKGLFYVTLLYSVIFLDESK 71

Query: 279 --DLNTLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLL 336
              L    VE++M K    + EDT +    +++ + NI  L VVDD  K +GI+   D++
Sbjct: 72  IKKLLGKKVEEIMTKKVITVDEDTTIEDVARIMSKKNIKRLPVVDD-GKLVGIISRGDII 130

Query: 337 RF 338
           R 
Sbjct: 131 RS 132



 Score = 36.8 bits (85), Expect = 0.008
 Identities = 18/42 (42%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 233 VKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR 274
           V     + D   I+S+K    + VVD+G KL GII+ GDI R
Sbjct: 91  VDEDTTIEDVARIMSKKNIKRLPVVDDG-KLVGIISRGDIIR 131



 Score = 34.5 bits (79), Expect = 0.039
 Identities = 15/47 (31%), Positives = 26/47 (55%)

Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
           K+   + +D  L   +++L    IS + VVD+  + +GIV   DL+R
Sbjct: 1   KDVITVKKDDTLRDVVEILLTGKISGVPVVDNEGRVVGIVSEGDLIR 47


>gnl|CDD|73100 cd04600, CBS_pair_HPP_assoc, This cd contains two tandem repeats of
           the cystathionine beta-synthase (CBS pair) domains
           associated with the HPP motif domain. These proteins are
           integral membrane proteins with four transmembrane
           spanning helices. The function of these proteins is
           uncertain, but they are thought to be transporters. CBS
           is a small domain originally identified in cystathionine
           beta-synthase and subsequently found in a wide range of
           different proteins. CBS domains usually come in tandem
           repeats, which associate to form a so-called Bateman
           domain or a CBS pair which is reflected in this model.
           The interface between the two CBS domains forms a cleft
           that is a potential ligand binding site. The CBS pair
           coexists with a variety of other functional domains.  It
           has been proposed that the CBS domain may play a
           regulatory role, although its exact function is
           unknown..
          Length = 124

 Score = 51.4 bits (123), Expect = 4e-07
 Identities = 29/111 (26%), Positives = 49/111 (44%), Gaps = 12/111 (10%)

Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDL------------NTLSV 285
            L +A  +L   R   + VVD  ++L GI+T+ D+ R+   D                +V
Sbjct: 12  SLEEAWALLRRHRIKALPVVDGDRRLVGIVTQRDLLRHARPDGRRPLRGRLRGRDKPETV 71

Query: 286 EDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLL 336
            D+M      +  DT +   + LL       + VVD+ ++ +GIV   DL+
Sbjct: 72  GDIMSPPVVTVRPDTPIAELVPLLADGGHHHVPVVDEDRRLVGIVTQTDLI 122



 Score = 41.4 bits (97), Expect = 4e-04
 Identities = 20/39 (51%), Positives = 24/39 (61%)

Query: 299 DTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
           DT L  A  LLR+H I  L VVD  ++ +GIV   DLLR
Sbjct: 10  DTSLEEAWALLRRHRIKALPVVDGDRRLVGIVTQRDLLR 48



 Score = 36.7 bits (85), Expect = 0.009
 Identities = 15/54 (27%), Positives = 29/54 (53%), Gaps = 2/54 (3%)

Query: 219 CASDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI 272
              D+M     +  V+   P+ + + +L++     V VVDE ++L GI+T+ D+
Sbjct: 70  TVGDIMSPP--VVTVRPDTPIAELVPLLADGGHHHVPVVDEDRRLVGIVTQTDL 121


>gnl|CDD|88401 cd04795, SIS, SIS domain. SIS (Sugar ISomerase) domains are found
           in many phosphosugar isomerases and phosphosugar binding
           proteins. SIS domains are also found in proteins that
           regulate the expression of genes involved in synthesis
           of phosphosugars..
          Length = 87

 Score = 51.1 bits (122), Expect = 4e-07
 Identities = 31/81 (38%), Positives = 45/81 (55%), Gaps = 2/81 (2%)

Query: 67  VVITGIGKSGHIGSKLASTLAS-TGTPSFFVHAAEASHGD-LGMITRDDLIIVLSWSGSS 124
           + + GIG SG I +  A  L   TG     + A E  H   L ++ + D++I LS+SG +
Sbjct: 1   IFVIGIGGSGAIAAYFALELLELTGIEVVALIATELEHASLLSLLRKGDVVIALSYSGRT 60

Query: 125 DELKAILYYARRFSIPLIAIT 145
           +EL A L  A+   IP+IAIT
Sbjct: 61  EELLAALEIAKELGIPVIAIT 81


>gnl|CDD|73102 cd04602, CBS_pair_IMPDH_2, This cd contains two tandem repeats of
           the cystathionine beta-synthase (CBS pair) domains in
           the inosine 5' monophosphate dehydrogenase (IMPDH)
           protein.  IMPDH is an essential enzyme that catalyzes
           the first step unique to GTP synthesis, playing a key
           role in the regulation of cell proliferation and
           differentiation. CBS is a small domain originally
           identified in cystathionine beta-synthase and
           subsequently found in a wide range of different
           proteins. CBS domains usually come in tandem repeats,
           which associate to form a so-called Bateman domain or a
           CBS pair which is reflected in this model. The interface
           between the two CBS domains forms a cleft that is a
           potential ligand binding site. The CBS pair coexists
           with a variety of other functional domains. It has been
           proposed that the CBS domain may play a regulatory role,
           although its exact function is unknown. Mutations of
           conserved residues within this domain in IMPDH have been
           associated with retinitis pigmentosa..
          Length = 114

 Score = 50.9 bits (122), Expect = 5e-07
 Identities = 28/102 (27%), Positives = 53/102 (51%), Gaps = 8/102 (7%)

Query: 241 DAITILSEKRFGCVAVVDEGQ---KLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVIL 297
           D + I  +K F  + V ++G+   KL GI+T  DI  +F  D +   + +VM     +++
Sbjct: 15  DVLEIKEKKGFSGIPVTEDGKSGGKLLGIVTSRDI--DFLTD-SETPLSEVMTPREVLVV 71

Query: 298 EDTLLTV--AMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
             T +T+  A ++LR+     L +V+D  + + +V   DL +
Sbjct: 72  APTGITLEEANEILRESKKGKLPIVNDDGELVALVTRSDLKK 113



 Score = 31.7 bits (72), Expect = 0.28
 Identities = 15/55 (27%), Positives = 30/55 (54%)

Query: 221 SDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRN 275
           S+VM   + + +   G  L +A  IL E + G + +V++  +L  ++T  D+ +N
Sbjct: 60  SEVMTPREVLVVAPTGITLEEANEILRESKKGKLPIVNDDGELVALVTRSDLKKN 114


>gnl|CDD|73144 cd04802, CBS_pair_3, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 112

 Score = 51.0 bits (122), Expect = 5e-07
 Identities = 33/108 (30%), Positives = 51/108 (47%), Gaps = 5/108 (4%)

Query: 233 VKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNF---HKDLNTLSVEDVM 289
           V     + +A  I++E   G + VVD   K  GIITE D+ +     +     + V +VM
Sbjct: 6   VDPDTTVYEAANIMTENNIGRLIVVDNE-KPVGIITERDLVKKVVSRNLKPREVPVGEVM 64

Query: 290 IKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
                 I  +  L  A +L+ +H I  L VVDD  + +GIV   D++ 
Sbjct: 65  STPLITIDPNASLNEAAKLMAKHGIKRLPVVDD-DELVGIVTTTDIVM 111



 Score = 29.4 bits (66), Expect = 1.4
 Identities = 16/47 (34%), Positives = 29/47 (61%), Gaps = 1/47 (2%)

Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
           KN   +  DT +  A  ++ ++NI  L+VVD+ +K +GI+   DL++
Sbjct: 1   KNVITVDPDTTVYEAANIMTENNIGRLIVVDN-EKPVGIITERDLVK 46


>gnl|CDD|32404 COG2222, AgaS, Predicted phosphosugar isomerases [Cell envelope
           biogenesis, outer membrane].
          Length = 340

 Score = 50.7 bits (121), Expect = 6e-07
 Identities = 32/120 (26%), Positives = 48/120 (40%), Gaps = 4/120 (3%)

Query: 66  RVVITGIGKSGHIGSKLASTLAS-TGTPSFFVHAAEASHGDLGMITRDDLIIVLSWSGSS 124
           R++  G G S H  +     L    G     + A+E        +  D L+I  S SG++
Sbjct: 41  RILFVGCGSSLHAATPAKYLLERELGLLVAAIPASEFLTNGAKYLGEDSLVIAFSQSGNT 100

Query: 125 DELKAILYYARRFSIPLIAITSENKSVVACHADIVLTLPKEPESCPHGLAPTTSAIMQLA 184
            E  A    A+      IA+T+E  S +A  AD V+      E+    +A T S    L 
Sbjct: 101 PESVAAAELAKEGGALTIALTNEEDSPLARAADYVIPYLAGEEA---SVAATKSFTASLL 157



 Score = 29.9 bits (67), Expect = 0.94
 Identities = 35/183 (19%), Positives = 68/183 (37%), Gaps = 22/183 (12%)

Query: 26  CALRSIIAEKRGLSSLESSLQG---ELSFQFHC-AVEKIKAIKGRVVITGIGKSGHIGSK 81
            AL +++AE  G + L ++L     E +      A E  +       I  +G     G+ 
Sbjct: 157 LALLALLAEYDGDAQLLAALPDLPLEAAKALEEDAQEFAEEYADEDRIYTLGSGPLYGAA 216

Query: 82  LASTLAS---TGTPSFFVHAAEASHGDLGMITRDDLIIVLSWSGSSDEL-KAILYYARRF 137
             + L         S  + + E  HG   ++     +++      + EL +  L + + +
Sbjct: 217 YEAALKLKEMQWIHSEAISSGEFRHGPKELVEEGTPVLLFVSEDETRELDERALKFLKNY 276

Query: 138 SIPLIAITSENKSVVACHADIVLTLPKEPESCPHGLAPTTSAIMQLAIGDALAIALLESR 197
              ++ I ++         D  L L  +     H LAP    ++ L +   LA AL  +R
Sbjct: 277 GAKVLVIDAK---------DAALDLIDQRVR--HDLAP---PLLSLVVAQRLAYALAVAR 322

Query: 198 NFS 200
             +
Sbjct: 323 GHN 325


>gnl|CDD|73103 cd04603, CBS_pair_KefB_assoc, This cd contains two tandem repeats
           of the cystathionine beta-synthase (CBS pair) domains
           associated with the KefB (Kef-type K+ transport systems)
           domain which is involved in inorganic ion transport and
           metabolism. CBS is a small domain originally identified
           in cystathionine beta-synthase and subsequently found in
           a wide range of different proteins. CBS domains usually
           come in tandem repeats, which associate to form a
           so-called Bateman domain or a CBS pair which is
           reflected in this model. The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains.  It has been proposed that the
           CBS domain may play a regulatory role, although its
           exact function is unknown..
          Length = 111

 Score = 49.5 bits (118), Expect = 1e-06
 Identities = 33/101 (32%), Positives = 54/101 (53%)

Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVIL 297
           PL +AI +++E     V VVDE  K+ G +T  D+      D  TL V +V I    ++ 
Sbjct: 11  PLREAIKMINELGARAVVVVDEENKVLGQVTLSDLLEIGPNDYETLKVCEVYIVPVPIVY 70

Query: 298 EDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
            D+ +T  +++ R+    V+ VVD   K +G ++  +LLRF
Sbjct: 71  CDSKVTDLLRIFRETEPPVVAVVDKEGKLVGTIYERELLRF 111



 Score = 33.7 bits (77), Expect = 0.066
 Identities = 20/64 (31%), Positives = 28/64 (43%), Gaps = 4/64 (6%)

Query: 211 GKLGTLFVCASDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEG 270
               TL VC   +      +P+V     + D + I  E     VAVVD+  KL G I E 
Sbjct: 51  NDYETLKVCEVYI----VPVPIVYCDSKVTDLLRIFRETEPPVVAVVDKEGKLVGTIYER 106

Query: 271 DIFR 274
           ++ R
Sbjct: 107 ELLR 110


>gnl|CDD|73133 cd04635, CBS_pair_22, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 122

 Score = 49.6 bits (118), Expect = 1e-06
 Identities = 28/104 (26%), Positives = 50/104 (48%), Gaps = 11/104 (10%)

Query: 245 ILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFH-----------KDLNTLSVEDVMIKNP 293
           ++ E  F  + VV +  +L GIIT  DI R              +   + +VE +M    
Sbjct: 18  LMLESGFTGLPVVQKAGELIGIITRRDIIRAGSVRTSVEDQQRTQTKASPTVEKIMSTPV 77

Query: 294 KVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
             +  D  +  A++L+ +H+I  L VV++  + +GIV   D+L+
Sbjct: 78  YSVTPDDSIATAVELMLEHDIGRLPVVNEKDQLVGIVDRHDVLK 121



 Score = 27.6 bits (61), Expect = 4.7
 Identities = 12/51 (23%), Positives = 23/51 (45%)

Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRFGII 341
           + P     D  ++    L+ +   + L VV    + IGI+   D++R G +
Sbjct: 1   REPVTCTPDDPVSKVWDLMLESGFTGLPVVQKAGELIGIITRRDIIRAGSV 51


>gnl|CDD|73131 cd04633, CBS_pair_20, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 121

 Score = 49.4 bits (118), Expect = 2e-06
 Identities = 35/117 (29%), Positives = 55/117 (47%), Gaps = 14/117 (11%)

Query: 233 VKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI------------FRNFHKDL 280
           V     +  A  ++ +     + V++ G KL GI+TE DI             R+  + +
Sbjct: 6   VSPDDRVSHARRLMLDHDISRLPVIEGG-KLVGIVTEKDIADALRSFRPLVRDRHQERRI 64

Query: 281 NTLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
             L V D+M +    I  DT ++    L+ ++NI  L VVDD  K +GIV   D+LR
Sbjct: 65  RNLPVSDIMTRPVITIEPDTSVSDVASLMLENNIGGLPVVDD-GKLVGIVTRTDILR 120


>gnl|CDD|73127 cd04629, CBS_pair_16, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 114

 Score = 49.0 bits (117), Expect = 2e-06
 Identities = 27/106 (25%), Positives = 51/106 (48%), Gaps = 9/106 (8%)

Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR-----NFHKDLNTLSVEDVMIKN 292
            + +A+  L + +     VVD+   L G ++E D  +     ++H D    +V D+M   
Sbjct: 11  SVTEAVEKLLKSKISGGPVVDDNGNLVGFLSEQDCLKQLLESSYHCDG-VATVRDIMTTE 69

Query: 293 PKVI-LEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
              +  +D+++ +A QL+ +       VVDD  K +G +   D+LR
Sbjct: 70  VLTVSPDDSIVDLA-QLMLKAKPKRYPVVDD-GKLVGQISRRDVLR 113



 Score = 31.6 bits (72), Expect = 0.33
 Identities = 15/48 (31%), Positives = 23/48 (47%)

Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
           +NP     D  +T A++ L +  IS   VVDD    +G +   D L+ 
Sbjct: 1   RNPVTFTPDMSVTEAVEKLLKSKISGGPVVDDNGNLVGFLSEQDCLKQ 48


>gnl|CDD|73109 cd04609, CBS_pair_PALP_assoc2, This cd contains two tandem repeats
           of the cystathionine beta-synthase (CBS pair) domains
           associated with the pyridoxal-phosphate (PALP) dependent
           enzyme domain upstream.   The vitamin B6 complex
           comprises pyridoxine, pyridoxal, and pyridoxamine, as
           well as the 5'-phosphate esters of pyridoxal (PALP) and
           pyridoxamine, the last two being the biologically active
           coenzyme derivatives.  The members of the PALP family
           are principally involved in the biosynthesis of amino
           acids and amino acid-derived metabolites, but they are
           also found in the biosynthetic pathways of amino sugars
           and other amine-containing compounds.  CBS is a small
           domain originally identified in cystathionine
           beta-synthase and subsequently found in a wide range of
           different proteins. CBS domains usually come in tandem
           repeats, which associate to form a so-called Bateman
           domain or a CBS pair which is reflected in this model.
           The interface between the two CBS domains forms a cleft
           that is a potential ligand binding site. The CBS pair
           coexists with a variety of other functional domains.  It
           has been proposed that the CBS domain may play a
           regulatory role, although its exact function is
           unknown..
          Length = 110

 Score = 49.0 bits (117), Expect = 2e-06
 Identities = 29/103 (28%), Positives = 51/103 (49%), Gaps = 5/103 (4%)

Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLN--TLSVEDVMIKNPKV 295
            +  AI  + E     + VVD+G ++ G I E D+     +     +L V +VM +    
Sbjct: 11  TVSQAIERMREYGVSQLPVVDDG-RVVGSIDESDLLDALIEGKAKFSLPVREVMGEPLPT 69

Query: 296 ILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
           +  D  +    +LL + N++V  VVD+  K +GI+   DLL++
Sbjct: 70  VDPDAPIEELSELLDRGNVAV--VVDEGGKFVGIITRADLLKY 110



 Score = 30.5 bits (69), Expect = 0.69
 Identities = 15/43 (34%), Positives = 26/43 (60%), Gaps = 2/43 (4%)

Query: 298 EDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRFGI 340
           +DT+   A++ +R++ +S L VVDD  + +G +   DLL   I
Sbjct: 9   DDTVSQ-AIERMREYGVSQLPVVDD-GRVVGSIDESDLLDALI 49



 Score = 29.4 bits (66), Expect = 1.5
 Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 4/55 (7%)

Query: 220 ASDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR 274
             +VM  G+ +P V    P+ +   +L   R     VVDEG K  GIIT  D+ +
Sbjct: 59  VREVM--GEPLPTVDPDAPIEELSELLD--RGNVAVVVDEGGKFVGIITRADLLK 109


>gnl|CDD|73125 cd04626, CBS_pair_13, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 111

 Score = 49.1 bits (117), Expect = 2e-06
 Identities = 28/100 (28%), Positives = 51/100 (51%), Gaps = 4/100 (4%)

Query: 239 LIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR--NFHKDLNTLSVEDVMIKNPKVI 296
           + +A+  + +     + V D  +KLKG++T  DI     F   L    V +++ ++   +
Sbjct: 12  IREALHEMLKYNTNEIIVKDNEEKLKGVVTFTDILDLDLFESFLE-KKVFNIVSQDVFYV 70

Query: 297 LEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLL 336
            E+  +  A+ ++R+  I  L VVDD  K IG+V   D+L
Sbjct: 71  NEEDTIDEALDIMREKQIGRLPVVDD-NKLIGVVRTKDIL 109



 Score = 32.9 bits (75), Expect = 0.15
 Identities = 13/45 (28%), Positives = 25/45 (55%)

Query: 295 VILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRFG 339
            I ED  +  A+  + ++N + ++V D+ +K  G+V F D+L   
Sbjct: 5   TIDEDASIREALHEMLKYNTNEIIVKDNEEKLKGVVTFTDILDLD 49


>gnl|CDD|73143 cd04801, CBS_pair_M50_like, This cd contains two tandem repeats of
           the cystathionine beta-synthase (CBS pair) domains in
           association with the metalloprotease peptidase M50.  CBS
           is a small domain originally identified in cystathionine
           beta-synthase and subsequently found in a wide range of
           different proteins. CBS domains usually come in tandem
           repeats, which associate to form a so-called Bateman
           domain or a CBS pair which is reflected in this model.
           The interface between the two CBS domains forms a cleft
           that is a potential ligand binding site. The CBS pair
           coexists with a variety of other functional domains.  It
           has been proposed that the CBS domain may play a
           regulatory role, although its exact function is
           unknown..
          Length = 114

 Score = 48.7 bits (116), Expect = 2e-06
 Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 4/88 (4%)

Query: 254 VAVVDEGQKLKGIITEGDIFR---NFHKDLNTLSVEDVMIKNPKVILEDTLLTVAMQLLR 310
             VVD   +  GII+  D+     +       + V     K   V+ E++L  V ++LL 
Sbjct: 28  FVVVDNEGRYVGIISLADLRAIPTSQWAQTTVIQVMTPAAKLVTVLSEESLAEV-LKLLE 86

Query: 311 QHNISVLMVVDDCQKAIGIVHFLDLLRF 338
           +  +  L VV+D  + IG++   DLLR 
Sbjct: 87  EQGLDELAVVEDSGQVIGLITEADLLRR 114



 Score = 33.6 bits (77), Expect = 0.081
 Identities = 15/53 (28%), Positives = 27/53 (50%)

Query: 222 DVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR 274
            VM     +  V     L + + +L E+    +AVV++  ++ G+ITE D+ R
Sbjct: 61  QVMTPAAKLVTVLSEESLAEVLKLLEEQGLDELAVVEDSGQVIGLITEADLLR 113


>gnl|CDD|73132 cd04634, CBS_pair_21, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 143

 Score = 48.3 bits (115), Expect = 3e-06
 Identities = 35/139 (25%), Positives = 52/139 (37%), Gaps = 36/139 (25%)

Query: 233 VKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIF------------------- 273
                 + DA  +L E +     V+D G KL GI++E DI                    
Sbjct: 6   CNADDTISDAARLLRENKISGAPVLDGG-KLVGIVSESDILKLLVTHDPSGNLWLPSPLE 64

Query: 274 ------RNFHK---------DLNTLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLM 318
                 R F           D   + V D+M K    I  D  +  A +L+ +H I  L 
Sbjct: 65  LIELPLREFINWEETKRALTDAGKMKVRDIMTKKVITISPDASIEDAAELMVRHKIKRLP 124

Query: 319 VVDDCQKAIGIVHFLDLLR 337
           VV+D  + +GIV   D++ 
Sbjct: 125 VVED-GRLVGIVTRGDIIE 142



 Score = 30.2 bits (68), Expect = 0.90
 Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 1/47 (2%)

Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
           KNP     D  ++ A +LLR++ IS   V+D   K +GIV   D+L+
Sbjct: 1   KNPITCNADDTISDAARLLRENKISGAPVLDG-GKLVGIVSESDILK 46


>gnl|CDD|32729 COG2905, COG2905, Predicted signal-transduction protein containing
           cAMP-binding and CBS domains [Signal transduction
           mechanisms].
          Length = 610

 Score = 48.4 bits (115), Expect = 3e-06
 Identities = 27/102 (26%), Positives = 46/102 (45%), Gaps = 3/102 (2%)

Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLN--TLSVEDVMIKNPKV 295
            + DA   + ++    + V+D+   L GI+T  D+      D    T  V +VM      
Sbjct: 167 SIQDAARKMKDEGVSSLVVLDDSGPLLGIVTRKDLRSRVIADGRSKTQKVSEVMTSPVIS 226

Query: 296 ILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
           +     L  AM ++ ++ I  L V +D Q  +GI+   D+LR
Sbjct: 227 VDRGDFLFEAMLMMLRNRIKHLPVTEDGQ-PLGILTLTDILR 267



 Score = 35.3 bits (81), Expect = 0.027
 Identities = 13/61 (21%), Positives = 24/61 (39%)

Query: 278 KDLNTLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
            +     V +V       +     +  A + ++   +S L+V+DD    +GIV   DL  
Sbjct: 144 SEFILTRVGEVKTLPAVTVSPQASIQDAARKMKDEGVSSLVVLDDSGPLLGIVTRKDLRS 203

Query: 338 F 338
            
Sbjct: 204 R 204



 Score = 33.7 bits (77), Expect = 0.077
 Identities = 32/109 (29%), Positives = 56/109 (51%), Gaps = 17/109 (15%)

Query: 220 ASDVMHSGDSIPLVKI--GCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFH 277
            S+VM S    P++ +  G  L +A+ ++   R   + V ++GQ L GI+T  DI R F 
Sbjct: 216 VSEVMTS----PVISVDRGDFLFEAMLMMLRNRIKHLPVTEDGQPL-GILTLTDILRLFS 270

Query: 278 KDLNTL--------SVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLM 318
           ++   L        S+E+  + N   +L+D+L T+  + +R   IS L+
Sbjct: 271 QNSIVLVKRIARASSIEE--LANTAELLDDSLSTLVSRGVRTEFISELI 317


>gnl|CDD|73106 cd04606, CBS_pair_Mg_transporter, This cd contains two tandem
           repeats of the cystathionine beta-synthase (CBS pair)
           domain in the magnesium transporter, MgtE.  MgtE and its
           homologs are found in eubacteria, archaebacteria, and
           eukaryota. Members of this family transport Mg2+ or
           other divalent cations into the cell via two highly
           conserved aspartates. CBS is a small domain originally
           identified in cystathionine beta-synthase and
           subsequently found in a wide range of different
           proteins. CBS domains usually come in tandem repeats,
           which associate to form a so-called Bateman domain or a
           CBS pair which is reflected in this model. The interface
           between the two CBS domains forms a cleft that is a
           potential ligand binding site. The CBS pair coexists
           with a variety of other functional domains. It has been
           proposed that the CBS domain may play a regulatory role,
           although its exact function is unknown..
          Length = 109

 Score = 47.8 bits (114), Expect = 4e-06
 Identities = 21/81 (25%), Positives = 41/81 (50%), Gaps = 4/81 (4%)

Query: 256 VVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNIS 315
           VVDE  +L G+++  D+      D +T  V D+M  +   +  D       +L  ++++ 
Sbjct: 30  VVDEEGRLLGVVSLRDLLLA---DPDTP-VSDIMDTDVISVSADDDQEEVARLFEKYDLL 85

Query: 316 VLMVVDDCQKAIGIVHFLDLL 336
            L VVD+  + +GI+   D++
Sbjct: 86  ALPVVDEEGRLVGIITVDDVI 106



 Score = 34.7 bits (80), Expect = 0.034
 Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 2/52 (3%)

Query: 221 SDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI 272
           SD+M     +  V       +   +  +     + VVDE  +L GIIT  D+
Sbjct: 56  SDIMD--TDVISVSADDDQEEVARLFEKYDLLALPVVDEEGRLVGIITVDDV 105



 Score = 28.9 bits (65), Expect = 2.1
 Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 5/48 (10%)

Query: 295 VILEDTLLTVAMQLLRQH-----NISVLMVVDDCQKAIGIVHFLDLLR 337
            + ED  +  A++ LR++      I  + VVD+  + +G+V   DLL 
Sbjct: 1   AVREDWTVGEALEYLRRNADDPETIYYIYVVDEEGRLLGVVSLRDLLL 48


>gnl|CDD|73120 cd04621, CBS_pair_8, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 135

 Score = 47.6 bits (113), Expect = 4e-06
 Identities = 28/124 (22%), Positives = 49/124 (39%), Gaps = 26/124 (20%)

Query: 239 LIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLN----------------- 281
           L+  +  + +   G V VVD+  K  G+IT  D+     +D                   
Sbjct: 12  LLHVVDEMEKNGVGRVIVVDDNGKPVGVITYRDLAFAEFEDNERGLPKKSIKMKRKAGQK 71

Query: 282 --------TLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFL 333
                    L  ED+M +    +  +  +  A +L+ + NIS L VVD+    +G++   
Sbjct: 72  RYRYVKEVPLVAEDIMTEEIITVSPNDDVVDAAKLMLEANISGLPVVDN-DNIVGVITKT 130

Query: 334 DLLR 337
           D+ R
Sbjct: 131 DICR 134


>gnl|CDD|30798 COG0449, GlmS, Glucosamine 6-phosphate synthetase, contains
           amidotransferase and phosphosugar isomerase domains
           [Cell envelope biogenesis, outer membrane].
          Length = 597

 Score = 47.5 bits (113), Expect = 6e-06
 Identities = 40/168 (23%), Positives = 66/168 (39%), Gaps = 10/168 (5%)

Query: 40  SLESSLQGELSFQFHCAVE-KIKAIKGRVVITGIGKSGH---IGSKLASTLASTGTPSFF 95
           +L ++LQG L       ++  I     R++I   G S H   +       LA        
Sbjct: 258 ALRNTLQGRLDELVQNELDLDILREVDRIIIVACGTSYHAGLVAKYFFERLAKIPV---E 314

Query: 96  VHAAEASHGDLGMITRDDLIIVLSWSGSSDELKAILYYARRFSIPLIAITSENKSVVACH 155
           V  A         +  + L+I +S SG + +  A L  A+      +AIT+   S +A  
Sbjct: 315 VEEASEFRYREPALNPNTLVIAISQSGETADTLAALRLAKEQGAKTLAITNVPGSTIARE 374

Query: 156 ADIVLTLPKEPESCPHGLAPTTSAIMQLAIGDALAIALLESRNFSEND 203
           +D  L +   PE    G+A T +   Q+     LA+ L + R     +
Sbjct: 375 SDHTLLIRAGPEI---GVASTKAFTAQVLALYLLALYLAKQRGTISEE 419


>gnl|CDD|73096 cd04596, CBS_pair_DRTGG_assoc, This cd contains two tandem repeats
           of the cystathionine beta-synthase (CBS pair) domains
           associated with a DRTGG domain upstream. The function of
           the DRTGG domain, named after its conserved residues, is
           unknown. CBS is a small domain originally identified in
           cystathionine beta-synthase and subsequently found in a
           wide range of different proteins. CBS domains usually
           come in tandem repeats, which associate to form a
           so-called Bateman domain or a CBS pair which is
           reflected in this model.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains. It has been proposed that the
           CBS domain may play a regulatory role, although its
           exact function is unknown..
          Length = 108

 Score = 47.1 bits (112), Expect = 6e-06
 Identities = 29/87 (33%), Positives = 43/87 (49%), Gaps = 7/87 (8%)

Query: 250 RFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILEDTLLTVAMQLL 309
           RF    VVDE  K+ GI+T  D+           ++E VM KNP  +   T +     ++
Sbjct: 27  RF---PVVDEKNKVVGIVTSKDVA----GKDPDTTIEKVMTKNPITVNPKTSVASVAHMM 79

Query: 310 RQHNISVLMVVDDCQKAIGIVHFLDLL 336
               I +L VVDD +K +GI+   D+L
Sbjct: 80  IWEGIEMLPVVDDNKKLLGIISRQDVL 106



 Score = 27.0 bits (60), Expect = 7.8
 Identities = 9/22 (40%), Positives = 15/22 (68%)

Query: 254 VAVVDEGQKLKGIITEGDIFRN 275
           + VVD+ +KL GII+  D+ + 
Sbjct: 87  LPVVDDNKKLLGIISRQDVLKA 108


>gnl|CDD|73118 cd04619, CBS_pair_6, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 114

 Score = 46.9 bits (111), Expect = 8e-06
 Identities = 29/108 (26%), Positives = 50/108 (46%), Gaps = 3/108 (2%)

Query: 233 VKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLN---TLSVEDVM 289
           + +   L  A  IL E     V V D   KL G++T+ D+ R   +      T  VE+VM
Sbjct: 6   IDVNATLQRAAKILGEPGIDLVVVCDPHGKLAGVLTKTDVVRQMGRCGGPGCTAPVENVM 65

Query: 290 IKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
            +         LL    Q+++Q  +  + VVD+  + +G+++  D L+
Sbjct: 66  TRAVVSCRPGDLLHDVWQVMKQRGLKNIPVVDENARPLGVLNARDALK 113


>gnl|CDD|32420 COG2239, MgtE, Mg/Co/Ni transporter MgtE (contains CBS domain)
           [Inorganic ion transport and metabolism].
          Length = 451

 Score = 45.6 bits (108), Expect = 2e-05
 Identities = 21/89 (23%), Positives = 43/89 (48%), Gaps = 4/89 (4%)

Query: 250 RFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILEDTLLTVAMQLL 309
               + VVDE  KL G+++  D+      +L    ++D+M  +   +L D       +L 
Sbjct: 167 TIYYLYVVDEKGKLLGVVSLRDLLTAEPDEL----LKDLMEDDVVSVLADDDQEEVARLF 222

Query: 310 RQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
            ++++  + VVD+  + IGI+   D++  
Sbjct: 223 EKYDLLAVPVVDEDNRLIGIITIDDIIDV 251


>gnl|CDD|32286 COG2103, COG2103, Predicted sugar phosphate isomerase [General
           function prediction only].
          Length = 298

 Score = 45.2 bits (107), Expect = 3e-05
 Identities = 35/137 (25%), Positives = 55/137 (40%), Gaps = 25/137 (18%)

Query: 56  AVEKI-KAIK--GRVVITGIGKSGHIGSKLASTLAST-------------GTPSFFVHAA 99
           AV+ I  A+K  GR++  G G SG +G   AS    T             G     + A 
Sbjct: 49  AVDIIAAALKQGGRLIYIGAGTSGRLGVLDASECPPTFGVPPELVIGLIAGGEEAILKAV 108

Query: 100 EASHGDLGM---------ITRDDLIIVLSWSGSSDELKAILYYARRFSIPLIAITSENKS 150
           E +  D  +         +T  D+++ ++ SG +  +   L YAR+     I I     S
Sbjct: 109 EGAEDDEELGEADLKNIGLTAKDVVVGIAASGRTPYVIGALEYARQRGATTIGIACNPGS 168

Query: 151 VVACHADIVLTLPKEPE 167
            ++  ADI +     PE
Sbjct: 169 AISRIADIAIEPVVGPE 185


>gnl|CDD|88404 cd05007, SIS_Etherase, N-acetylmuramic acid 6-phosphate etherase.
           Members of this family contain the SIS (Sugar ISomerase)
           domain. The SIS domain is found in many phosphosugar
           isomerases and phosphosugar binding proteins. The
           bacterial cell wall sugar N-acetylmuramic acid carries a
           unique D-lactyl ether substituent at the C3 position.
           The etherase catalyzes the cleavage of the lactyl ether
           bond of N-acetylmuramic acid 6-phosphate..
          Length = 257

 Score = 45.1 bits (107), Expect = 3e-05
 Identities = 41/134 (30%), Positives = 55/134 (41%), Gaps = 23/134 (17%)

Query: 56  AVEKIKAIKGRVVITGIGKSGHIGSKLASTLAST-GTPSFFVHA---------------- 98
           A E+++A  GR++  G G SG +G   AS L  T GTP   V                  
Sbjct: 42  AAERLRA-GGRLIYVGAGTSGRLGVLDASELPPTFGTPPERVVGLIAGGEPALTRAVEGA 100

Query: 99  ---AEASHGDLGMI--TRDDLIIVLSWSGSSDELKAILYYARRFSIPLIAITSENKSVVA 153
               EA   DL  I  T  D++I ++ SG +  +   L YAR      I I     S + 
Sbjct: 101 EDDEEAGAADLQAINLTERDVVIGIAASGRTPYVLGALRYARARGALTIGIACNPGSPLL 160

Query: 154 CHADIVLTLPKEPE 167
             ADI + L   PE
Sbjct: 161 QLADIAIALITGPE 174


>gnl|CDD|33866 COG4109, COG4109, Predicted transcriptional regulator containing
           CBS domains [Transcription].
          Length = 432

 Score = 44.9 bits (106), Expect = 4e-05
 Identities = 26/116 (22%), Positives = 52/116 (44%), Gaps = 4/116 (3%)

Query: 222 DVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLN 281
           D+M   +    ++    + D + ++ +       VV+   K+ G++T  D+         
Sbjct: 192 DIMTPLEDTSYLRETDTVEDWLDLVEKTGHSRFPVVNRSMKVVGVVTMRDVLDK----KP 247

Query: 282 TLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
           + ++E VM KNP  +   T +    Q++    I +L VVD     +GI+   D+L+
Sbjct: 248 STTIEKVMTKNPITVRAKTSVASVAQMMIWEGIEMLPVVDSNNTLLGIITRQDVLK 303


>gnl|CDD|33419 COG3620, COG3620, Predicted transcriptional regulator with
           C-terminal CBS domains [Transcription].
          Length = 187

 Score = 44.1 bits (104), Expect = 5e-05
 Identities = 34/125 (27%), Positives = 62/125 (49%), Gaps = 9/125 (7%)

Query: 218 VCASDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR--- 274
           + A  +MHS   +  V     + D + ++ +K    + V++E  K+ G ITE DI R   
Sbjct: 65  ITAKTIMHS--PVVSVSPDDSISDVVNLMRDKGISQLPVIEED-KVVGSITENDIVRALL 121

Query: 275 NFHKDLNTLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLD 334
              + + +L V +VM +    +  D  L V  QLL +H    ++VV++  K +GI+   D
Sbjct: 122 EGMESIRSLRVREVMGEPFPTVSPDESLNVISQLLEEHP--AVLVVEN-GKVVGIITKAD 178

Query: 335 LLRFG 339
           +++  
Sbjct: 179 IMKLL 183


>gnl|CDD|36975 KOG1764, KOG1764, KOG1764, 5'-AMP-activated protein kinase, gamma
           subunit [Energy production and conversion].
          Length = 381

 Score = 43.9 bits (103), Expect = 7e-05
 Identities = 29/112 (25%), Positives = 52/112 (46%), Gaps = 12/112 (10%)

Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI--------FRNFHKDLNTLSVEDVM 289
           P+I+A+ I+SE+R   + VVDE  K  G  +  D+        + N      + ++    
Sbjct: 247 PVIEALKIMSERRISALPVVDENGKKVGNYSRFDVIHLAREGTYNNLDLSCLSEALSHRP 306

Query: 290 IKNPKVIL---EDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
           I+   V+      TL  V  +L+  H +  L VVD+    +G++   D+L +
Sbjct: 307 IRFEGVVTCRPTSTLAEVIDKLVA-HRVHRLWVVDEDGVLVGVISLSDILSY 357



 Score = 41.2 bits (96), Expect = 4e-04
 Identities = 36/161 (22%), Positives = 67/161 (41%), Gaps = 15/161 (9%)

Query: 183 LAIGDALAIALLESRNFSENDFYVLHPGGKLGTLFVCASDVMHSGDSIPLVKIGCP--LI 240
           L I D + + L   ++ S  D   +    +L         ++      P V I     L+
Sbjct: 116 LTITDFITVLLRYYKSKSSLDNIEVLEDSQLSKR-REVECLLKETLKPPFVSISPESSLL 174

Query: 241 DAITILSEKRFGCVAVVDEGQ-KLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPK----- 294
           DA+ +L + R   V V+D    ++  I+T+  I +    +   L +  ++ K+       
Sbjct: 175 DAVLLLIKSRIHRVPVIDPETGEVLYILTQRRILKFLWLNGRLLPLPSLLSKSLSDLGIG 234

Query: 295 ------VILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGI 329
                  I EDT +  A++++ +  IS L VVD+  K +G 
Sbjct: 235 TWSNIASISEDTPVIEALKIMSERRISALPVVDENGKKVGN 275


>gnl|CDD|73114 cd04614, CBS_pair_1, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 96

 Score = 43.3 bits (102), Expect = 1e-04
 Identities = 25/108 (23%), Positives = 48/108 (44%), Gaps = 15/108 (13%)

Query: 230 IPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVM 289
           +P V    PL  A+ I+       + V+D+  KL GIITE D+              +V+
Sbjct: 3   VPTVWEETPLPVAVRIMELANVKALPVLDDDGKLSGIITERDLIAK----------SEVV 52

Query: 290 IKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
               +  + +       Q ++++ I  + +++   K IG++   DLL+
Sbjct: 53  TATKRTTVSE-----CAQKMKRNRIEQIPIINGNDKLIGLLRDHDLLK 95



 Score = 29.1 bits (65), Expect = 1.8
 Identities = 16/47 (34%), Positives = 27/47 (57%)

Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
           +N   + E+T L VA++++   N+  L V+DD  K  GI+   DL+ 
Sbjct: 1   RNVPTVWEETPLPVAVRIMELANVKALPVLDDDGKLSGIITERDLIA 47


>gnl|CDD|73137 cd04639, CBS_pair_26, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 111

 Score = 42.9 bits (101), Expect = 1e-04
 Identities = 19/76 (25%), Positives = 34/76 (44%)

Query: 255 AVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNI 314
            VVD    L G++T  D+ R   +      V  VM ++   +     L   ++L++Q   
Sbjct: 28  PVVDGDGHLVGLLTRDDLIRALAEGGPDAPVRGVMRRDFPTVSPSATLDAVLRLMQQGGA 87

Query: 315 SVLMVVDDCQKAIGIV 330
             + VVD   + +G+V
Sbjct: 88  PAVPVVDGSGRLVGLV 103



 Score = 30.6 bits (69), Expect = 0.61
 Identities = 22/103 (21%), Positives = 38/103 (36%), Gaps = 21/103 (20%)

Query: 185 IGDALAIALLESRNFSENDFYVLHPGGKL---------------GTLFVCASDVMHSGDS 229
           + DA   ALL +   ++++F V+   G L               G        VM     
Sbjct: 12  LDDAAD-ALLAT---TQHEFPVVDGDGHLVGLLTRDDLIRALAEGGPDAPVRGVMRRD-- 65

Query: 230 IPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI 272
            P V     L   + ++ +     V VVD   +L G++T  ++
Sbjct: 66  FPTVSPSATLDAVLRLMQQGGAPAVPVVDGSGRLVGLVTLENV 108


>gnl|CDD|73090 cd04590, CBS_pair_CorC_HlyC_assoc, This cd contains two tandem
           repeats of the cystathionine beta-synthase (CBS pair)
           domains associated with the CorC_HlyC domain. CorC_HlyC
           is a transporter associated domain. This small domain is
           found in Na+/H+ antiporters, in proteins involved in
           magnesium and cobalt efflux, and in association with
           some proteins of unknown function.  The function of the
           CorC_HlyC domain is uncertain but it might be involved
           in modulating transport of ion substrates. CBS is a
           small domain originally identified in cystathionine
           beta-synthase and subsequently found in a wide range of
           different proteins. CBS domains usually come in tandem
           repeats, which associate to form a so-called Bateman
           domain or a CBS pair which is reflected in this model.
           The interface between the two CBS domains forms a cleft
           that is a potential ligand binding site. The CBS pair
           coexists with a variety of other functional domains. It
           has been proposed that the CBS domain may play a
           regulatory role, although its exact function is unknown.
           The second CBS domain in this CD is degenerate..
          Length = 111

 Score = 42.4 bits (100), Expect = 2e-04
 Identities = 21/100 (21%), Positives = 45/100 (45%), Gaps = 2/100 (2%)

Query: 238 PLIDAITILSEKRFGCVAVVDEG-QKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVI 296
            L + + +++E       V D     + G++   D+ R   +    L + D +++ P  +
Sbjct: 11  TLEEILELIAESGHSRFPVYDGDLDNIIGVVHVKDLLRALAEGEEDLDLRD-LLRPPLFV 69

Query: 297 LEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLL 336
            E T L   ++ +R+    + +VVD+     G+V   D+L
Sbjct: 70  PESTPLDDLLEEMRKERSHMAIVVDEYGGTAGLVTLEDIL 109



 Score = 26.6 bits (59), Expect = 9.2
 Identities = 13/43 (30%), Positives = 19/43 (44%)

Query: 230 IPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI 272
              V    PL D +  + ++R     VVDE     G++T  DI
Sbjct: 66  PLFVPESTPLDDLLEEMRKERSHMAIVVDEYGGTAGLVTLEDI 108


>gnl|CDD|73116 cd04617, CBS_pair_4, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 118

 Score = 42.5 bits (100), Expect = 2e-04
 Identities = 28/108 (25%), Positives = 54/108 (50%), Gaps = 7/108 (6%)

Query: 229 SIPL-VKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNF--HKDLNTLSV 285
           S P+ V+    + DAI  L  +  G + VVDE   L G+++  D+ +      DL  + V
Sbjct: 1   SPPVVVRENTSVYDAIVTLFLEDVGSLFVVDEDGDLVGVVSRKDLLKASIGGADLQKVPV 60

Query: 286 EDVMIKNPKVIL---EDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIV 330
             +M + P +     E+++L  A +L+ +H +  L VV+   + + ++
Sbjct: 61  GVIMTRMPNITTTTPEESVLEAAKKLI-EHQVDSLPVVEKVDEGLEVI 107



 Score = 28.2 bits (63), Expect = 3.6
 Identities = 15/45 (33%), Positives = 25/45 (55%)

Query: 293 PKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
           P V+ E+T +  A+  L   ++  L VVD+    +G+V   DLL+
Sbjct: 3   PVVVRENTSVYDAIVTLFLEDVGSLFVVDEDGDLVGVVSRKDLLK 47


>gnl|CDD|73089 cd04589, CBS_pair_CAP-ED_DUF294_assoc_bac, This cd contains two
           tandem repeats of the cystathionine beta-synthase (CBS
           pair) domains associated with the bacterial CAP_ED (cAMP
           receptor protein effector domain) family of
           transcription factors and the DUF294 domain.  Members of
           CAP_ED, include CAP which binds cAMP, FNR (fumarate and
           nitrate reductase) which uses an iron-sulfur cluster to
           sense oxygen, and CooA a heme containing CO sensor. In
           all cases binding of the effector leads to
           conformational changes and the ability to activate
           transcription. DUF294 is a putative
           nucleotidyltransferase with a conserved DxD motif. CBS
           is a small domain originally identified in cystathionine
           beta-synthase and subsequently found in a wide range of
           different proteins. CBS domains usually come in tandem
           repeats, which associate to form a so-called Bateman
           domain or a CBS pair which is reflected in this model.
           CBS domains usually come in tandem repeats, which
           associate to form a so-called Bateman domain or a CBS
           pair which is reflected in this model.  The interface
           between the two CBS domains forms a cleft that is a
           potential ligand binding site. The CBS pair coexists
           with a variety of other functional domains. It has been
           proposed that the CBS domain may play a regulatory role,
           although its exact function is unknown..
          Length = 111

 Score = 41.7 bits (98), Expect = 3e-04
 Identities = 26/103 (25%), Positives = 44/103 (42%), Gaps = 4/103 (3%)

Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVIL 297
            + DA  ++ E     + V D   +L GI+T  D+      D    S     I    +I 
Sbjct: 11  SIRDAARLMREHGADALLVRDGDPRL-GIVTRTDLLDAVLLDGLPSSTPVGEIATFPLIT 69

Query: 298 --EDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
              D  L  A+ L+ +H I  ++V +   + +G++   DLL F
Sbjct: 70  VDPDDFLFNALLLMTRHRIHRVVVREG-GEVVGVLEQTDLLSF 111


>gnl|CDD|88412 cd05017, SIS_PGI_PMI_1, The members of this protein family contain
           the SIS (Sugar ISomerase) domain and have both the
           phosphoglucose isomerase (PGI) and the phosphomannose
           isomerase (PMI) functions. These functions catalyze the
           reversible reactions of glucose 6-phosphate to fructose
           6-phosphate, and mannose 6-phosphate to fructose
           6-phosphate, respectively at an equal rate. This protein
           contains two SIS domains. This alignment is based on the
           first SIS domain..
          Length = 119

 Score = 41.7 bits (98), Expect = 3e-04
 Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 3/81 (3%)

Query: 66  RVVITGIGKSGHIGSKLASTLASTGTPSFFVHAAEASHGDLGMITRDDLIIVLSWSGSSD 125
            +VI G+G SG  G  L S L        +V      +     + R  L+I +S+SG+++
Sbjct: 1   NIVILGMGGSGIGGDLLESLLLDEAKIPVYVVK---DYTLPAFVDRKTLVIAVSYSGNTE 57

Query: 126 ELKAILYYARRFSIPLIAITS 146
           E  + +  A+     ++AITS
Sbjct: 58  ETLSAVEQAKERGAKIVAITS 78


>gnl|CDD|73140 cd04642, CBS_pair_29, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 126

 Score = 41.8 bits (98), Expect = 3e-04
 Identities = 22/116 (18%), Positives = 42/116 (36%), Gaps = 15/116 (12%)

Query: 238 PLIDAITILSEKRFGCVAVVDEGQK---------LKGIITEGDIFRNFHKDLNTLSVED- 287
            ++DA  ++ +     + VVDE  K         LKG++   D    +         E  
Sbjct: 11  RVLDAFKLMRKNNISGLPVVDEKGKLIGNISASDLKGLLLSPDDLLLYRTITFKELSEKF 70

Query: 288 -----VMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
                V  +        + L   +  L  + +  + VVD+  K IG++   D++  
Sbjct: 71  TDSDGVKSRPLITCTPSSTLKEVITKLVANKVHRVWVVDEEGKPIGVITLTDIISI 126



 Score = 31.4 bits (71), Expect = 0.38
 Identities = 17/40 (42%), Positives = 24/40 (60%)

Query: 296 ILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDL 335
           I  D  +  A +L+R++NIS L VVD+  K IG +   DL
Sbjct: 6   IDSDERVLDAFKLMRKNNISGLPVVDEKGKLIGNISASDL 45


>gnl|CDD|73108 cd04608, CBS_pair_PALP_assoc, This cd contains two tandem repeats
           of the cystathionine beta-synthase (CBS pair) domains
           associated with the pyridoxal-phosphate (PALP) dependent
           enzyme domain upstream.   The vitamin B6 complex
           comprises pyridoxine, pyridoxal, and pyridoxamine, as
           well as the 5'-phosphate esters of pyridoxal (PALP) and
           pyridoxamine, the last two being the biologically active
           coenzyme derivatives.  The members of the PALP family
           are principally involved in the biosynthesis of amino
           acids and amino acid-derived metabolites, but they are
           also found in the biosynthetic pathways of amino sugars
           and other amine-containing compounds.  CBS is a small
           domain originally identified in cystathionine
           beta-synthase and subsequently found in a wide range of
           different proteins. CBS domains usually come in tandem
           repeats, which associate to form a so-called Bateman
           domain or a CBS pair which is reflected in this model.
           The interface between the two CBS domains forms a cleft
           that is a potential ligand binding site. The CBS pair
           coexists with a variety of other functional domains.  It
           has been proposed that the CBS domain may play a
           regulatory role, although its exact function is
           unknown..
          Length = 124

 Score = 41.4 bits (97), Expect = 4e-04
 Identities = 32/109 (29%), Positives = 50/109 (45%), Gaps = 11/109 (10%)

Query: 241 DAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLS--VEDVMIK-NPKVIL 297
           +AI IL EK F  + VVDE  K+ G++T G++  +        S  V   + K   +V  
Sbjct: 15  EAIEILKEKGFDQLPVVDESGKILGMVTLGNLLSSLSSGKVQPSDPVSKALYKQFKRVNK 74

Query: 298 EDTLLTVAMQLLRQHNISVL--------MVVDDCQKAIGIVHFLDLLRF 338
            DTL  ++  L     + V         +  +  +K IGIV  +DLL +
Sbjct: 75  NDTLGKLSRILETDAFLLVFFEQISSAAIGKEKQEKPIGIVTKIDLLSY 123



 Score = 28.3 bits (63), Expect = 3.1
 Identities = 14/49 (28%), Positives = 25/49 (51%)

Query: 290 IKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
           +K P  +L       A+++L++     L VVD+  K +G+V   +LL  
Sbjct: 1   LKAPVTVLPTVTCAEAIEILKEKGFDQLPVVDESGKILGMVTLGNLLSS 49


>gnl|CDD|73139 cd04641, CBS_pair_28, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 120

 Score = 41.3 bits (97), Expect = 4e-04
 Identities = 27/111 (24%), Positives = 54/111 (48%), Gaps = 11/111 (9%)

Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIF---RNFHKDLNTLSVEDVMIKNP- 293
           PLID + +L E+R   + +VDE  K+  + +  D+    +    +   L+V + + +   
Sbjct: 11  PLIDVLDMLVERRVSALPIVDENGKVVDVYSRFDVINLAKEGAYNNLDLTVGEALERRSQ 70

Query: 294 ------KVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338
                     +D L T+   L+ +  +  L+VVD+ ++  GI+   D+L+F
Sbjct: 71  DFEGVRTCSPDDCLRTI-FDLIVKARVHRLVVVDENKRVEGIISLSDILQF 120


>gnl|CDD|37761 KOG2550, KOG2550, KOG2550, IMP dehydrogenase/GMP reductase
           [Nucleotide transport and metabolism].
          Length = 503

 Score = 41.1 bits (96), Expect = 4e-04
 Identities = 29/78 (37%), Positives = 42/78 (53%), Gaps = 3/78 (3%)

Query: 260 GQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMV 319
           G KL GIIT  DI   F +D + L V DVM KNP    +   L  A ++L++     L V
Sbjct: 151 GSKLVGIITSRDI--QFLEDNSLL-VSDVMTKNPVTGAQGITLKEANEILKKIKKGKLPV 207

Query: 320 VDDCQKAIGIVHFLDLLR 337
           VDD  + + ++   DL++
Sbjct: 208 VDDKGELVAMLSRTDLMK 225


>gnl|CDD|73097 cd04597, CBS_pair_DRTGG_assoc2, This cd contains two tandem repeats
           of the cystathionine beta-synthase (CBS pair) domains
           associated with a DRTGG domain upstream. The function of
           the DRTGG domain, named after its conserved residues, is
           unknown. CBS is a small domain originally identified in
           cystathionine beta-synthase and subsequently found in a
           wide range of different proteins. CBS domains usually
           come in tandem repeats, which associate to form a
           so-called Bateman domain or a CBS pair which is
           reflected in this model. The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains. It has been proposed that the
           CBS domain may play a regulatory role, although its
           exact function is unknown..
          Length = 113

 Score = 41.0 bits (96), Expect = 5e-04
 Identities = 20/53 (37%), Positives = 27/53 (50%)

Query: 285 VEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
           V DV+ + P     +  L  A+ L+ +HNI  L VVDD     GI+  LDL  
Sbjct: 60  VRDVINRKPVTARPNDPLREALNLMHEHNIRTLPVVDDDGTPAGIITLLDLAE 112



 Score = 33.3 bits (76), Expect = 0.11
 Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 2/54 (3%)

Query: 222 DVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRN 275
           DV++        +   PL +A+ ++ E     + VVD+     GIIT  D+   
Sbjct: 62  DVIN--RKPVTARPNDPLREALNLMHEHNIRTLPVVDDDGTPAGIITLLDLAEK 113


>gnl|CDD|73092 cd04592, CBS_pair_EriC_assoc_euk, This cd contains two tandem
           repeats of the cystathionine beta-synthase (CBS pair)
           domains in the EriC CIC-type chloride channels in
           eukaryotes. These ion channels are proteins with a
           seemingly simple task of allowing the passive flow of
           chloride ions across biological membranes. CIC-type
           chloride channels come from all kingdoms of life, have
           several gene families, and can be gated by voltage. The
           members of the CIC-type chloride channel are
           double-barreled: two proteins forming homodimers at a
           broad interface formed by four helices from each
           protein. The two pores are not found at this interface,
           but are completely contained within each subunit, as
           deduced from the mutational analyses, unlike many other
           channels, in which four or five identical or
           structurally related subunits jointly form one pore. CBS
           is a small domain originally identified in cystathionine
           beta-synthase and subsequently found in a wide range of
           different proteins. CBS domains usually come in tandem
           repeats, which associate to form a so-called Bateman
           domain or a CBS pair which is reflected in this model.
           The interface between the two CBS domains forms a cleft
           that is a potential ligand binding site. The CBS pair
           coexists with a variety of other functional domains. It
           has been proposed that the CBS domain may play a
           regulatory role, although its exact function is unknown.
           Mutations of conserved residues within this domain in
           CLC chloride channel family members have been associated
           with classic Bartter syndrome, Osteopetrosis, Dent's
           disease, idiopathic generalized epilepsy, and myotonia..
          Length = 133

 Score = 40.0 bits (93), Expect = 0.001
 Identities = 31/110 (28%), Positives = 44/110 (40%), Gaps = 22/110 (20%)

Query: 233 VKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR-------------NFHKD 279
           V     L +A+ ++ +++  CV VVD    L+GI+T GDI R             +  K 
Sbjct: 6   VSPTTTLKEALNLMLDEKQSCVLVVDSDDFLEGILTLGDIQRFLFTNKTTRVQPEDETKQ 65

Query: 280 LNTLSVEDVMIKN---------PKVILEDTLLTVAMQLLRQHNISVLMVV 320
            NT  V  V  K                DT LT A +L+    +  L VV
Sbjct: 66  TNTCLVSSVCTKGISYGGQECGLWTCTPDTDLTTAKKLMEAKGVKQLPVV 115


>gnl|CDD|73110 cd04610, CBS_pair_ParBc_assoc, This cd contains two tandem repeats
           of the cystathionine beta-synthase (CBS pair) domains
           associated with a ParBc (ParB-like nuclease) domain
           downstream. CBS is a small domain originally identified
           in cystathionine beta-synthase and subsequently found in
           a wide range of different proteins. CBS domains usually
           come in tandem repeats, which associate to form a
           so-called Bateman domain or a CBS pair which is
           reflected in this model. The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains.  It has been proposed that the
           CBS domain may play a regulatory role, although its
           exact function is unknown..
          Length = 107

 Score = 38.3 bits (89), Expect = 0.003
 Identities = 28/97 (28%), Positives = 50/97 (51%), Gaps = 5/97 (5%)

Query: 241 DAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILEDT 300
           D I ++ E       VVD   K+ GI++  D+     KD +   VE++M K+  V + + 
Sbjct: 15  DVIKLIKETGHDGFPVVD-NGKVVGIVSARDLL---GKDPDET-VEEIMSKDLVVAVPEM 69

Query: 301 LLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
            +  A +++ +  IS L VVD+    +GI+   D++R
Sbjct: 70  DIMDAARVMFRTGISKLPVVDENNNLVGIITNTDVIR 106



 Score = 26.8 bits (59), Expect = 9.0
 Identities = 13/37 (35%), Positives = 20/37 (54%)

Query: 239 LIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRN 275
           ++DA  ++       + VVDE   L GIIT  D+ R+
Sbjct: 71  IMDAARVMFRTGISKLPVVDENNNLVGIITNTDVIRS 107


>gnl|CDD|73130 cd04632, CBS_pair_19, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 128

 Score = 38.4 bits (89), Expect = 0.003
 Identities = 31/117 (26%), Positives = 50/117 (42%), Gaps = 17/117 (14%)

Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLN---------------T 282
            +  AI +L E     + VVD+  KL GI+T  DI     +D +                
Sbjct: 11  SVGKAINVLREHGISRLPVVDDNGKLTGIVTRHDIVDFVVRDRDKARTGDRSGEKERMLD 70

Query: 283 LSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVV--DDCQKAIGIVHFLDLLR 337
           L V D M         +  +  A+  + +++ S ++VV  DD  K +GI+   D+LR
Sbjct: 71  LPVYDAMSSPVITASPNDSVRDAVDRMLENDDSSVVVVTPDDDTKVVGILTKKDVLR 127



 Score = 34.2 bits (78), Expect = 0.055
 Identities = 19/43 (44%), Positives = 26/43 (60%)

Query: 298 EDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRFGI 340
           ED  +  A+ +LR+H IS L VVDD  K  GIV   D++ F +
Sbjct: 8   EDDSVGKAINVLREHGISRLPVVDDNGKLTGIVTRHDIVDFVV 50


>gnl|CDD|33251 COG3448, COG3448, CBS-domain-containing membrane protein [Signal
           transduction mechanisms].
          Length = 382

 Score = 38.0 bits (88), Expect = 0.003
 Identities = 28/103 (27%), Positives = 47/103 (45%), Gaps = 7/103 (6%)

Query: 241 DAITILSEKRFGCVAVVDEGQKLKGIITEGDIF----RNFHKDLNTL---SVEDVMIKNP 293
            A  +L E R   + V+DE ++L GI+T+ D+      +  + L  L   +V+ +M    
Sbjct: 266 HARKLLQEHRIKALPVLDEHRRLVGIVTQRDLLKHARPSPFQRLRFLRPPTVKGIMTTPV 325

Query: 294 KVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLL 336
             +  DT     +  L    +  L V+D   K +GIV   DL+
Sbjct: 326 VTVRPDTPAVELVPRLADEGLHALPVLDAAGKLVGIVSQTDLI 368



 Score = 38.0 bits (88), Expect = 0.003
 Identities = 19/56 (33%), Positives = 34/56 (60%)

Query: 282 TLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
            L+  D+M ++   +  DT +  A +LL++H I  L V+D+ ++ +GIV   DLL+
Sbjct: 244 ELTCADIMSRDVVTVSTDTSIDHARKLLQEHRIKALPVLDEHRRLVGIVTQRDLLK 299



 Score = 33.0 bits (75), Expect = 0.12
 Identities = 9/45 (20%), Positives = 25/45 (55%)

Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNT 282
           P ++ +  L+++    + V+D   KL GI+++ D+    +++ + 
Sbjct: 333 PAVELVPRLADEGLHALPVLDAAGKLVGIVSQTDLIAALYRNWSQ 377


>gnl|CDD|31445 COG1253, TlyC, Hemolysins and related proteins containing CBS
           domains [General function prediction only].
          Length = 429

 Score = 37.2 bits (86), Expect = 0.007
 Identities = 21/120 (17%), Positives = 49/120 (40%), Gaps = 2/120 (1%)

Query: 218 VCASDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQK-LKGIITEGDIFRNF 276
               ++M     I  + +   + + I ++ E     + V D     + GI+   D+ R  
Sbjct: 206 RTVREIMTPRTDIVALDLTDTVEELIELILESGHSRIPVYDGDLDNIIGIVHVKDLLRAL 265

Query: 277 HKDLNTLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLL 336
               + L +  + ++ P  + E   L+  ++  R+    + +VVD+     G+V   D++
Sbjct: 266 LDGQSDLDLRVL-VRPPLFVPETLSLSDLLEEFREERTHMAIVVDEYGGVEGLVTLEDII 324



 Score = 31.8 bits (72), Expect = 0.25
 Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 3/62 (4%)

Query: 279 DLNTLSVEDVMIKNPKVIL--EDTLLTVAMQLLRQHNISVLMVVDDCQKAI-GIVHFLDL 335
           DL+  +V ++M     ++       +   ++L+ +   S + V D     I GIVH  DL
Sbjct: 202 DLDDRTVREIMTPRTDIVALDLTDTVEELIELILESGHSRIPVYDGDLDNIIGIVHVKDL 261

Query: 336 LR 337
           LR
Sbjct: 262 LR 263


>gnl|CDD|73098 cd04598, CBS_pair_GGDEF_assoc, This cd contains two tandem repeats
           of the cystathionine beta-synthase (CBS pair) domains in
           association with the GGDEF (DiGuanylate-Cyclase (DGC))
           domain. The GGDEF domain has been suggested to be
           homologous to the adenylyl cyclase catalytic domain and
           is thought to be involved in regulating cell surface
           adhesiveness in bacteria. CBS is a small domain
           originally identified in cystathionine beta-synthase and
           subsequently found in a wide range of different
           proteins. CBS domains usually come in tandem repeats,
           which associate to form a so-called Bateman domain or a
           CBS pair which is reflected in this model. The interface
           between the two CBS domains forms a cleft that is a
           potential ligand binding site. The CBS pair coexists
           with a variety of other functional domains. It has been
           proposed that the CBS domain may play a regulatory role,
           although its exact function is unknown..
          Length = 119

 Score = 36.3 bits (84), Expect = 0.012
 Identities = 24/92 (26%), Positives = 42/92 (45%), Gaps = 9/92 (9%)

Query: 254 VAVVDEGQKLKGIITEGDIFR----NFHKDLNT-LSVEDVMIKNPKVILEDTLLTVAMQL 308
           +AVVD+G+ + G+I    +       + + L     V +VM  +P ++  DT L    +L
Sbjct: 28  LAVVDDGRPV-GLIMREALMELLSTPYGRALYGKKPVSEVMDPDPLIVEADTPLEEVSRL 86

Query: 309 L---RQHNISVLMVVDDCQKAIGIVHFLDLLR 337
                  N+    +V +  + +GI    DLLR
Sbjct: 87  ATGRDSQNLYDGFIVTEEGRYLGIGTVKDLLR 118


>gnl|CDD|73093 cd04593, CBS_pair_EriC_assoc_bac_arch, This cd contains two tandem
           repeats of the cystathionine beta-synthase (CBS pair)
           domains in the EriC CIC-type chloride channels in
           bacteria and archaea. These ion channels are proteins
           with a seemingly simple task of allowing the passive
           flow of chloride ions across biological membranes.
           CIC-type chloride channels come from all kingdoms of
           life, have several gene families, and can be gated by
           voltage. The members of the CIC-type chloride channel
           are double-barreled: two proteins forming homodimers at
           a broad interface formed by four helices from each
           protein. The two pores are not found at this interface,
           but are completely contained within each subunit, as
           deduced from the mutational analyses, unlike many other
           channels, in which four or five identical or
           structurally related subunits jointly form one pore. CBS
           is a small domain originally identified in cystathionine
           beta-synthase and subsequently found in a wide range of
           different proteins. CBS domains usually come in tandem
           repeats, which associate to form a so-called Bateman
           domain or a CBS pair which is reflected in this model.
           The interface between the two CBS domains forms a cleft
           that is a potential ligand binding site. The CBS pair
           coexists with a variety of other functional domains. It
           has been proposed that the CBS domain may play a
           regulatory role, although its exact function is unknown.
           Mutations of conserved residues within this domain in
           CLC chloride channel family members have been associated
           with classic Bartter syndrome, Osteopetrosis, Dent's
           disease, idiopathic generalized epilepsy, and myotonia..
          Length = 115

 Score = 35.7 bits (82), Expect = 0.017
 Identities = 16/44 (36%), Positives = 22/44 (50%)

Query: 231 PLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR 274
           P++    PL +A   L E + G   VVD    + GIIT  D+ R
Sbjct: 4   PVLSATTPLREAAEQLIESKHGSALVVDRDGGVVGIITLPDLLR 47



 Score = 33.4 bits (76), Expect = 0.11
 Identities = 15/45 (33%), Positives = 21/45 (46%)

Query: 293 PKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
           P V+   T L  A + L +      +VVD     +GI+   DLLR
Sbjct: 3   PPVLSATTPLREAAEQLIESKHGSALVVDRDGGVVGIITLPDLLR 47


>gnl|CDD|73138 cd04640, CBS_pair_27, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 126

 Score = 34.8 bits (80), Expect = 0.036
 Identities = 18/50 (36%), Positives = 29/50 (58%)

Query: 292 NPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRFGII 341
            P VI  DT +  A++L+ +H + +L+VVD     IG++  +DLL    I
Sbjct: 2   KPIVIPADTSIDEALELMIKHGVRLLLVVDSDDNFIGVITAVDLLGEEPI 51


>gnl|CDD|88403 cd05006, SIS_GmhA, Phosphoheptose isomerase is a member of the SIS
           (Sugar ISomerase) superfamily. Phosphoheptose isomerase
           catalyzes the isomerization of sedoheptulose 7-phosphate
           into D-glycero-D-mannoheptose 7-phosphate. This is the
           first step of the biosynthesis of gram-negative bacteria
           inner core lipopolysaccharide precursor,
           L-glycero-D-mannoheptose (Gmh)..
          Length = 177

 Score = 34.3 bits (79), Expect = 0.049
 Identities = 15/51 (29%), Positives = 27/51 (52%)

Query: 113 DLIIVLSWSGSSDELKAILYYARRFSIPLIAITSENKSVVACHADIVLTLP 163
           D++I +S SG+S  +   L  A+   +  IA+T  +   +   ADI + +P
Sbjct: 103 DVLIGISTSGNSPNVLKALEAAKERGMKTIALTGRDGGKLLELADIEIHVP 153


>gnl|CDD|73082 cd04582, CBS_pair_ABC_OpuCA_assoc, This cd contains two tandem
           repeats of the cystathionine beta-synthase (CBS pair)
           domains in association with the ABC transporter OpuCA.
           OpuCA is the ATP binding component of a bacterial solute
           transporter that serves a protective role to cells
           growing in a hyperosmolar environment but the function
           of the CBS domains in OpuCA remains unknown.  In the
           related ABC transporter, OpuA, the tandem CBS domains
           have been shown to function as sensors for ionic
           strength, whereby they control the transport activity
           through an electronic switching mechanism. ABC
           transporters are a large family of proteins involved in
           the transport of a wide variety of different compounds,
           like sugars, ions, peptides, and more complex organic
           molecules. They are a subset of nucleotide hydrolases
           that contain a signature motif, Q-loop, and
           H-loop/switch region, in addition to the Walker A
           motif/P-loop and Walker B motif commonly found in a
           number of ATP- and GTP-binding and hydrolyzing proteins.
           CBS is a small domain originally identified in
           cystathionine beta-synthase and subsequently found in a
           wide range of different proteins. CBS domains usually
           come in tandem repeats, which associate to form a
           so-called Bateman domain or a CBS pair which is
           reflected in this model. The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains.  It has been proposed that the
           CBS domain may play a regulatory role, although its
           exact function is unknown..
          Length = 106

 Score = 34.1 bits (78), Expect = 0.064
 Identities = 20/102 (19%), Positives = 39/102 (38%), Gaps = 5/102 (4%)

Query: 229 SIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDV 288
               V+   PL DA+ ++ +     + VVD   +  G +T  +         +     D 
Sbjct: 2   EPITVRPDDPLSDALGLMDDSDLRALTVVDADGQPLGFVTRREA-----ARASGGCCGDH 56

Query: 289 MIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIV 330
                  +  D  L + +  +  H++S L  VD+  + +G V
Sbjct: 57  AEPFKVTVSVDDDLRIVLSRMFAHDMSWLPCVDEDGRYVGEV 98


>gnl|CDD|88414 cd05710, SIS_1, A subgroup of the SIS domain. SIS (Sugar ISomerase)
           domains are found in many phosphosugar isomerases and
           phosphosugar binding proteins. SIS domains are also
           found in proteins that regulate the expression of genes
           involved in synthesis of phosphosugars..
          Length = 120

 Score = 33.2 bits (76), Expect = 0.095
 Identities = 22/78 (28%), Positives = 38/78 (48%)

Query: 92  PSFFVHAAEASHGDLGMITRDDLIIVLSWSGSSDELKAILYYARRFSIPLIAITSENKSV 151
           P F  +AAE  H     +T   ++I+ S SG++ E  A   +A+     +I +T +  S 
Sbjct: 28  PVFVYNAAEFLHTGPKRLTEKSVVILASHSGNTKETVAAAKFAKEKGATVIGLTDDEDSP 87

Query: 152 VACHADIVLTLPKEPESC 169
           +A  AD V+    E ++ 
Sbjct: 88  LAKLADYVIVYGFEIDAV 105


>gnl|CDD|73128 cd04630, CBS_pair_17, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 114

 Score = 33.2 bits (76), Expect = 0.11
 Identities = 21/101 (20%), Positives = 43/101 (42%), Gaps = 5/101 (4%)

Query: 241 DAITILSEKRFGCVAVVDEG-QKLKGIITEGDIFRNF---HKDLNTLSVEDVMIKNPKVI 296
           +A+ ++ E     + V         GI+T  DI +      +D + ++V ++M K    +
Sbjct: 14  EALQLMKEHGVSSLVVEKRRESDAYGIVTMRDILKKVVAEGRDPDRVNVYEIMTKPLISV 73

Query: 297 LEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337
             D  +    +L+ + NI     V +  + IGI+   D+  
Sbjct: 74  SPDMDIKYCARLMERTNI-RRAPVVENNELIGIISLTDIFL 113


>gnl|CDD|88406 cd05009, SIS_GlmS_GlmD_2, SIS (Sugar ISomerase) domain repeat 2
           found in Glucosamine 6-phosphate synthase (GlmS) and
           Glucosamine-6-phosphate deaminase (GlmD). The SIS domain
           is found in many phosphosugar isomerases and
           phosphosugar binding proteins. GlmS contains a
           N-terminal glutaminase domain and two C-terminal SIS
           domains and catalyzes the first step in hexosamine
           metabolism, converting fructose 6-phosphate into
           glucosamine 6-phosphate using glutamine as nitrogen
           source. The glutaminase domain hydrolyzes glutamine to
           glutamate and ammonia. Ammonia is transferred through a
           channel to the isomerase domain for glucosamine
           6-phosphate synthesis. The end product of the pathway is
           N-acetylglucosamine, which plays multiple roles in
           eukaryotic cells including being a building block of
           bacterial and fungal cell walls. In the absence of
           glutamine, GlmS catalyzes the isomerization of fructose
           6-phosphate into glucose 6- phosphate (PGI-like
           activity). Glucosamine-6-phosphate deaminase (GlmD)
           contains two SIS domains and catalyzes the deamination
           and isomerization of glucosamine-6-phosphate into
           fructose-6-phosphate with the release of ammonia; in
           presence of high ammonia concentration, GlmD can
           catalyze the reverse reaction..
          Length = 153

 Score = 31.4 bits (71), Expect = 0.37
 Identities = 21/112 (18%), Positives = 46/112 (41%), Gaps = 11/112 (9%)

Query: 89  TGTPSFFVHAAEASHGDLGMITRDDLIIVLSWSGSSDEL-KAILYYARRFSIPLIAITSE 147
           +   +    A E  HG + ++     +I L+     +E  ++++   +     +I IT +
Sbjct: 39  SYIHAEAYSAGEFKHGPIALVDEGTPVIFLAPEDRLEEKLESLIKEVKARGAKVIVITDD 98

Query: 148 NKSVVACHADIVLTLPKEPESCPHGLAPTTSAI-MQLAIGDALAIALLESRN 198
             +     AD+V+ +P   E     L+P    + +QL    A  +A+    +
Sbjct: 99  GDA--KDLADVVIRVPATVEE----LSPLLYIVPLQL---LAYHLAVARGID 141


>gnl|CDD|34183 COG4536, CorB, Putative Mg2+ and Co2+ transporter CorB [Inorganic
           ion transport and metabolism].
          Length = 423

 Score = 30.9 bits (70), Expect = 0.46
 Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 3/63 (4%)

Query: 279 DLNTLSVEDVMIKNPKVI---LEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDL 335
           DL  L+V D+M+   ++I   ++D    +  QLL   +  + +  DD    IG++H  DL
Sbjct: 196 DLENLTVSDIMVPRNEIIGIDIDDPWEEIVRQLLHSPHTRIPLYRDDLDNIIGVLHVRDL 255

Query: 336 LRF 338
           LR 
Sbjct: 256 LRL 258


>gnl|CDD|73091 cd04591, CBS_pair_EriC_assoc_euk_bac, This cd contains two tandem
           repeats of the cystathionine beta-synthase (CBS pair)
           domains in the EriC CIC-type chloride channels in
           eukaryotes and bacteria. These ion channels are proteins
           with a seemingly simple task of allowing the passive
           flow of chloride ions across biological membranes.
           CIC-type chloride channels come from all kingdoms of
           life, have several gene families, and can be gated by
           voltage. The members of the CIC-type chloride channel
           are double-barreled: two proteins forming homodimers at
           a broad interface formed by four helices from each
           protein. The two pores are not found at this interface,
           but are completely contained within each subunit, as
           deduced from the mutational analyses, unlike many other
           channels, in which four or five identical or
           structurally related subunits jointly form one pore. CBS
           is a small domain originally identified in cystathionine
           beta-synthase and subsequently found in a wide range of
           different proteins. CBS domains usually come in tandem
           repeats, which associate to form a so-called Bateman
           domain or a CBS pair which is reflected in this model.
           The interface between the two CBS domains forms a cleft
           that is a potential ligand binding site. The CBS pair
           coexists with a variety of other functional domains. It
           has been proposed that the CBS domain may play a
           regulatory role, although its exact function is unknown.
           Mutations of conserved residues within this domain in
           CLC chloride channel family members have been associated
           with classic Bartter syndrome, Osteopetrosis, Dent's
           disease, idiopathic generalized epilepsy, and myotonia..
          Length = 105

 Score = 30.2 bits (68), Expect = 0.75
 Identities = 20/85 (23%), Positives = 35/85 (41%), Gaps = 10/85 (11%)

Query: 254 VAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILEDTLLTVAMQLLRQHN 313
           V   +E  +L G I    +       ++          +P  +   T L    QL R+  
Sbjct: 31  VDSTEESPRLVGYILRSQLVVALKNYIDP---------SPFTVSPRTSLEKVHQLFRKLG 81

Query: 314 ISVLMVVDDCQKAIGIVHFLDLLRF 338
           +  L+VVD+  + +GI+   DLL+ 
Sbjct: 82  LRHLLVVDE-GRLVGIITRKDLLKA 105


>gnl|CDD|31322 COG1125, OpuBA, ABC-type proline/glycine betaine transport systems,
           ATPase components [Amino acid transport and metabolism].
          Length = 309

 Score = 29.1 bits (65), Expect = 1.9
 Identities = 18/68 (26%), Positives = 27/68 (39%), Gaps = 6/68 (8%)

Query: 274 RNFHKDLNTLSVEDVMIKNPKVILEDTLLTVA-----MQLLRQHNISVLMVVDDCQKAIG 328
               + L+ +SV D + +      E  L            L +   SVL VVD+  + +G
Sbjct: 240 ERGLRLLSLVSVADAVRRGEPADGEPLLEGFVDRDALSDFLARG-RSVLPVVDEDGRPLG 298

Query: 329 IVHFLDLL 336
            V   DLL
Sbjct: 299 TVTRADLL 306


>gnl|CDD|35695 KOG0474, KOG0474, KOG0474, Cl- channel CLC-7 and related proteins
           (CLC superfamily) [Inorganic ion transport and
           metabolism].
          Length = 762

 Score = 28.7 bits (64), Expect = 2.1
 Identities = 21/99 (21%), Positives = 36/99 (36%), Gaps = 4/99 (4%)

Query: 246 LSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHK---DLN-TLSVEDVMIKNPKVILEDTL 301
           + E R      V      +          + H    ++   + +   M  +P  + E   
Sbjct: 649 VEESRSTFDLPVRRKFTFRDFAKREPSIEDVHLTSEEMEMYVDLHPFMNPSPYTVPETMS 708

Query: 302 LTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRFGI 340
           L  A  L RQ  +  L+VV    + +GI+   DL R+ I
Sbjct: 709 LAKAFILFRQLGLRHLLVVPKTNRVVGILTRKDLARYRI 747


>gnl|CDD|73126 cd04627, CBS_pair_14, The CBS domain, named after human CBS, is a
           small domain originally identified in cystathionine
           beta-synthase and is subsequently found in a wide range
           of different proteins. CBS domains usually occur in
           tandem repeats. They associate to form a so-called
           Bateman domain or a CBS pair based on crystallographic
           studies in bacteria.  The CBS pair was used as a basis
           for this cd hierarchy since the human CBS proteins can
           adopt the typical core structure and form an
           intramolecular CBS pair.  The interface between the two
           CBS domains forms a cleft that is a potential ligand
           binding site. The CBS pair coexists with a variety of
           other functional domains and this has been used to help
           in its classification here.  It has been proposed that
           the CBS domain may play a regulatory role, although its
           exact function is unknown. Mutations of conserved
           residues within this domain are associated with a
           variety of human hereditary diseases, including
           congenital myotonia, idiopathic generalized epilepsy,
           hypercalciuric nephrolithiasis, and classic Bartter
           syndrome (CLC chloride channel family members),
           Wolff-Parkinson-White syndrome (gamma 2 subunit of
           AMP-activated protein kinase), retinitis pigmentosa (IMP
           dehydrogenase-1), and homocystinuria (cystathionine
           beta-synthase)..
          Length = 123

 Score = 28.7 bits (64), Expect = 2.4
 Identities = 14/35 (40%), Positives = 20/35 (57%)

Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI 272
           PLIDA+ ++  +    VAVVD    L G I+  D+
Sbjct: 86  PLIDALHLMHNEGISSVAVVDNQGNLIGNISVTDV 120


>gnl|CDD|33915 COG4175, ProV, ABC-type proline/glycine betaine transport system,
           ATPase component [Amino acid transport and metabolism].
          Length = 386

 Score = 28.4 bits (63), Expect = 2.7
 Identities = 25/104 (24%), Positives = 37/104 (35%), Gaps = 7/104 (6%)

Query: 176 TTSAIMQLA-------IGDALAIALLESRNFSENDFYVLHPGGKLGTLFVCASDVMHSGD 228
           T   IM+          GD   +AL   R+      Y +  G K   +    S V  +  
Sbjct: 275 TAKDIMRRPDLLIRKTPGDGPRVALKLLRDEGREYGYAVDRGNKFVGVVSIDSLVKAALI 334

Query: 229 SIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI 272
              L       +  I     +    VAVVDE  +  GII+ G++
Sbjct: 335 DDVLTVDADTPLSEILARIRQAPCPVAVVDEDGRYVGIISRGEL 378


>gnl|CDD|31264 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General
           function prediction only].
          Length = 339

 Score = 27.9 bits (62), Expect = 4.7
 Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 1/32 (3%)

Query: 56  AVEKIKAIKG-RVVITGIGKSGHIGSKLASTL 86
           A++K     G  V + G G  GH+  + A  +
Sbjct: 158 ALKKANVKPGKWVAVVGAGGLGHMAVQYAKAM 189


>gnl|CDD|173900 cd00674, LysRS_core_class_I, catalytic core domain of  class I
           lysyl tRNA synthetase.  Class I lysyl tRNA synthetase
           (LysRS) catalytic core domain. This class I enzyme is a
           monomer which aminoacylates the 2'-OH of the nucleotide
           at the 3' of the appropriate tRNA. The core domain is
           based on the Rossman fold and is responsible for the
           ATP-dependent formation of the enzyme bound
           aminoacyl-adenylate. It contains the characteristic
           class I HIGH and KMSKS motifs, which are involved in ATP
           binding. The class I LysRS is found only in archaea and
           some bacteria and has evolved separately from class II
           LysRS, as the two do not share structural or sequence
           similarity.
          Length = 353

 Score = 27.3 bits (61), Expect = 6.6
 Identities = 19/66 (28%), Positives = 25/66 (37%), Gaps = 15/66 (22%)

Query: 57  VEKIKAIKGRVVITGIGKSG--HIGSKLASTLASTGTPSFFVHAAEASHGDLGMITRDDL 114
           +E+ K  +  VV +GI  SG  HIG           T      A      DLG   R   
Sbjct: 12  IEERKGKEKYVVASGISPSGHIHIG-----NFREVITADLVARALR----DLGFEVR--- 59

Query: 115 IIVLSW 120
            ++ SW
Sbjct: 60  -LIYSW 64


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.323    0.138    0.397 

Gapped
Lambda     K      H
   0.267   0.0718    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,955,295
Number of extensions: 204884
Number of successful extensions: 839
Number of sequences better than 10.0: 1
Number of HSP's gapped: 742
Number of HSP's successfully gapped: 163
Length of query: 341
Length of database: 6,263,737
Length adjustment: 94
Effective length of query: 247
Effective length of database: 4,232,491
Effective search space: 1045425277
Effective search space used: 1045425277
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 58 (26.1 bits)