RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780426|ref|YP_003064839.1| hemolysin protein [Candidatus Liberibacter asiaticus str. psy62] (320 letters) >gnl|CDD|31445 COG1253, TlyC, Hemolysins and related proteins containing CBS domains [General function prediction only]. Length = 429 Score = 184 bits (469), Expect = 3e-47 Identities = 91/250 (36%), Positives = 141/250 (56%), Gaps = 14/250 (5%) Query: 67 EGIFSETEKEIFNNILRFRKIRIDDIMISRVSINAVEDKATVYEAMLMFEKYGRSWMPVY 126 EG+ E E+E+ NN+L + +IM R I A++ TV E + + + G S +PVY Sbjct: 186 EGVLEEEEREMINNVLDLDDRTVREIMTPRTDIVALDLTDTVEELIELILESGHSRIPVY 245 Query: 127 KNSLDNPRGMVHMRDVISYISHMYAKTNNINLNIQLSESNLIKNILFVPSSMLVSDLLTN 186 LDN G+VH++D++ + ++ L L++ LFVP ++ +SDLL Sbjct: 246 DGDLDNIIGIVHVKDLLRAL---------LDGQSDLDLRVLVRPPLFVPETLSLSDLLEE 296 Query: 187 IQESRIRMALVIDEHGGTDGLVSYEDIVSVLMRDITSEHHSKKSM-ISAVSDNTFIVDAR 245 +E R MA+V+DE+GG +GLV+ EDI+ ++ +I EH + I D+ ++VD R Sbjct: 297 FREERTHMAIVVDEYGGVEGLVTLEDIIEEIVGEIPDEHDEDEEEDIIQRDDDGWLVDGR 356 Query: 246 TDLEELAKIIGTDCNCLKGEQDVDSLGGLIFSVLDRIPARGEVVLEIPGFEIVILDADVR 305 LEEL +++G D L E+D D++ GL+ S+L RIP GE V I G +LD D R Sbjct: 357 VPLEELEELLGID---LDEEEDYDTIAGLVLSLLGRIPKVGESV-VIGGLRFEVLDMDGR 412 Query: 306 CVRRVRIRRL 315 + +V I RL Sbjct: 413 RIDKVLIVRL 422 >gnl|CDD|34183 COG4536, CorB, Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]. Length = 423 Score = 124 bits (313), Expect = 3e-29 Identities = 66/252 (26%), Positives = 124/252 (49%), Gaps = 18/252 (7%) Query: 67 EGIFSETEKEIFNNILRFRKIRIDDIMISR---VSINAVEDKATVYEAMLMFEKYGRSWM 123 EG ++ ++++ +L + + DIM+ R + I+ + + L+ + R + Sbjct: 180 EGSVNKIDRDMLLGVLDLENLTVSDIMVPRNEIIGIDIDDPWEEIVRQ-LLHSPHTR--I 236 Query: 124 PVYKNSLDNPRGMVHMRDVISYISHMYAKTNNINLNIQLSESNLIKNILFVPSSMLVSDL 183 P+Y++ LDN G++H+RD++ + K +I FVP +SD Sbjct: 237 PLYRDDLDNIIGVLHVRDLLRL---LNEKNEFTKEDI----LRAADEPYFVPEGTPLSDQ 289 Query: 184 LTNIQESRIRMALVIDEHGGTDGLVSYEDIVSVLMRDITSEHHSKKSMISAVSDNTFIVD 243 L Q ++ +ALV+DE+G GLV+ EDI+ ++ D T EH + + SD +FI+D Sbjct: 290 LVAFQRNKKHIALVVDEYGDIQGLVTLEDILEEIVGDFTDEHDTLAKEVIPQSDGSFIID 349 Query: 244 ARTDLEELAKIIGTDCNCLKGEQDVDSLGGLIFSVLDRIPARGEVVLEIPGFEIVILDAD 303 ++ +L + + + +D ++ GL+ L+ IP G+ V I G+ I IL Sbjct: 350 GSANVRDLNRALDWNLPD----EDARTINGLVLEELEEIPEEGQAV-RIGGYRIDILKVQ 404 Query: 304 VRCVRRVRIRRL 315 +++V+I L Sbjct: 405 ENRIKQVKITPL 416 >gnl|CDD|34182 COG4535, CorC, Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]. Length = 293 Score = 123 bits (310), Expect = 6e-29 Identities = 66/254 (25%), Positives = 126/254 (49%), Gaps = 15/254 (5%) Query: 63 DASLEGIFSETEKEIFNNILRFRKIRIDDIMISRVSINAVEDKATVYEAMLMFEKYGRSW 122 D+ + ++ ++ +R+ DIMI R + ++ T+ E + + + S Sbjct: 43 DSEQNELIDADTLDMLEGVMDIADLRVRDIMIPRSQMITLKRNQTLDECLDVIIESAHSR 102 Query: 123 MPVYKNSLDNPRGMVHMRDVISYISHMYAKTNNINLNIQLSESNLIKNILFVPSSMLVSD 182 PV D+ G++ +D++ + M + ++ L++ + VP S V Sbjct: 103 FPVISEDKDHVEGILLAKDLLPF---MRSDAEPFDI------KELLRPAVVVPESKRVDR 153 Query: 183 LLTNIQESRIRMALVIDEHGGTDGLVSYEDIVSVLMRDITSEHHSKKSM-ISAVSDNTFI 241 LL + R MA+VIDE GG GLV+ EDI+ ++ DI E+ ++ I +S +T+ Sbjct: 154 LLKEFRSQRNHMAIVIDEFGGVSGLVTIEDILEQIVGDIEDEYDEEEDADIRQLSRHTWR 213 Query: 242 VDARTDLEELAKIIGTDCNCLKGEQDVDSLGGLIFSVLDRIPARGEVVLEIPGFEIVILD 301 V A T++E+ + GT + +++VD++GGL+ +PARGE + +I G++ + Sbjct: 214 VRALTEIEDFNEAFGTHFS----DEEVDTIGGLVMQAFGHLPARGEKI-DIGGYQFKVAR 268 Query: 302 ADVRCVRRVRIRRL 315 AD R V ++ + Sbjct: 269 ADSRRVIQLHVTVP 282 >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 = 89.0 bits (221), Expect = 1e-18 Identities = 41/116 (35%), Positives = 66/116 (56%), Gaps = 9/116 (7%) Query: 99 INAVEDKATVYEAMLMFEKYGRSWMPVYKNSLDNPRGMVHMRDVISYISHMYAKTNNINL 158 I A++ T+ E + + + G S PVY LDN G+VH++D++ ++ Sbjct: 3 IVALDADDTLEEILELIAESGHSRFPVYDGDLDNIIGVVHVKDLLRALA---------EG 53 Query: 159 NIQLSESNLIKNILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIV 214 L +L++ LFVP S + DLL +++ R MA+V+DE+GGT GLV+ EDI+ Sbjct: 54 EEDLDLRDLLRPPLFVPESTPLDDLLEEMRKERSHMAIVVDEYGGTAGLVTLEDIL 109 >gnl|CDD|146225 pfam03471, CorC_HlyC, Transporter associated domain. This small domain is found in a family of proteins with the pfam01595 domain and two CBS domains with this domain found at the C-terminus of the proteins, the domain is also found at the C terminus of some Na+/H+ antiporters. This domain is also found in CorC that is involved in Magnesium and cobalt efflux. The function of this domain is uncertain but might be involved in modulating transport of ion substrates. Length = 80 Score = 72.2 bits (178), Expect = 2e-13 Identities = 28/82 (34%), Positives = 52/82 (63%), Gaps = 5/82 (6%) Query: 235 VSDNTFIVDARTDLEELAKIIGTDCNCLKGEQDVDSLGGLIFSVLDRIPARGE-VVLEIP 293 + D +++VD R L++L +++G D L E+D D+L GL+ +L RIP G+ V +++ Sbjct: 3 LDDGSYLVDGRAPLDDLNELLGLD---LP-EEDYDTLAGLVLELLGRIPEVGDKVEVDLG 58 Query: 294 GFEIVILDADVRCVRRVRIRRL 315 G +L+ D R +++VR+ +L Sbjct: 59 GLRFTVLEVDGRRIKKVRVTKL 80 >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 = 42.4 bits (99), Expect = 2e-04 Identities = 24/115 (20%), Positives = 50/115 (43%), Gaps = 7/115 (6%) Query: 102 VEDKATVYEAMLMFEKYGRSWMPVYKNSLDNPRGMVHMRDVISYISHMYAKTNNINLNIQ 161 V TV EA+ + ++G S +PV + G+V RD++ ++ ++ Sbjct: 6 VSPDDTVAEALRLMLEHGISGLPVV-DDDGRLVGIVTERDLLRALAEGGLDPLVTVGDV- 63 Query: 162 LSESNLIKNILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIVSV 216 + ++++ V + + + E IR V+D+ G G+V+ DI+ Sbjct: 64 -----MTRDVVTVSPDTSLEEAAELMLEHGIRRLPVVDDEGRLVGIVTRSDILRA 113 Score = 37.8 bits (87), Expect = 0.004 Identities = 18/87 (20%), Positives = 39/87 (44%), Gaps = 3/87 (3%) Query: 169 KNILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIVSVLMRDITSEHHSK 228 ++++ V V++ L + E I V+D+ G G+V+ D++ L + Sbjct: 1 RDVVTVSPDDTVAEALRLMLEHGISGLPVVDDDGRLVGIVTERDLLRALAEGGLDPLVTV 60 Query: 229 KSMISAVSDNTFIVDARTDLEELAKII 255 + ++ + V T LEE A+++ Sbjct: 61 GDV---MTRDVVTVSPDTSLEEAAELM 84 >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 = 39.1 bits (92), Expect = 0.002 Identities = 13/52 (25%), Positives = 27/52 (51%) Query: 168 IKNILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIVSVLMR 219 +++ VP + + L ++E+ I V+DE G G+V+ D++ L+ Sbjct: 6 TPDVVTVPPDTSLEEALELMRENGISRLPVVDEDGKLVGIVTLRDLLRALLG 57 Score = 35.6 bits (83), Expect = 0.020 Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 3/60 (5%) Query: 89 IDDIMISRVSINAVEDKATVYEAMLMFEKYGRSWMPVYKNSLDNPRGMVHMRDVISYISH 148 + DIM V V ++ EA+ + + G S +PV G+V +RD++ + Sbjct: 1 VKDIMTPDVVT--VPPDTSLEEALELMRENGISRLPVVDED-GKLVGIVTLRDLLRALLG 57 >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 = 37.8 bits (88), Expect = 0.004 Identities = 19/84 (22%), Positives = 36/84 (42%), Gaps = 3/84 (3%) Query: 63 DASLEGIFSETE-KEIFNNILRFRKIRIDDIMISRVSINAVEDKATVYEAMLMFEKYGRS 121 D L GI S + +EI + + + DIM + V + ++ +A+ FE Sbjct: 33 DGRLVGIVSLDDIREILFDPSLYDLVVASDIMTKPPVV--VYPEDSLEDALKKFEDSDYE 90 Query: 122 WMPVYKNSLDNPRGMVHMRDVISY 145 +PV + G++ D++S Sbjct: 91 QLPVVDDDPGKLLGILSRSDLLSA 114 Score = 30.1 bits (68), Expect = 0.85 Identities = 14/49 (28%), Positives = 27/49 (55%) Query: 169 KNILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIVSVL 217 ++++ +P +++LL I S V+D+ G G+VS +DI +L Sbjct: 1 RDVVTIPEDTPLNELLDVIAHSPENNFPVVDDDGRLVGIVSLDDIREIL 49 >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 = 36.3 bits (84), Expect = 0.010 Identities = 23/115 (20%), Positives = 46/115 (40%), Gaps = 7/115 (6%) Query: 106 ATVYEAMLMFEKYGRSWMPVYKNSLDNPRGMVHMRDVISYISHMYAKTNNINLNIQLSES 165 + EA + + G +PV G++ D++ Y+ K N I L Sbjct: 10 TPIMEAAKIMVRNGFRRLPVVDEGTGKLVGIITATDILKYLGGGE-KFNKIKTGNGLEAI 68 Query: 166 N------LIKNILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIV 214 N + +N++ + + D + E R+ V+D+ G G+V+ D++ Sbjct: 69 NEPVRSIMTRNVITITPDDSIKDAAELMLEKRVGGLPVVDDDGKLVGIVTERDLL 123 >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 = 35.9 bits (83), Expect = 0.017 Identities = 28/115 (24%), Positives = 57/115 (49%), Gaps = 6/115 (5%) Query: 101 AVEDKATVYEAMLMFEKYGRSWMPVYKNSLDNPRGMVHMRDVISYISHMYAKTNNINLNI 160 ++ ATV EA+ + +++G S + V K + G+V MRD+ + + A+ + + + Sbjct: 5 TIDGLATVAEALQLMKEHGVSSLVVEKRRESDAYGIVTMRDI---LKKVVAEGRDPD-RV 60 Query: 161 QLSESNLIKNILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIVS 215 + E + K ++ V M + ++ + IR A V+ E+ G++S DI Sbjct: 61 NVYEI-MTKPLISVSPDMDIKYCARLMERTNIRRAPVV-ENNELIGIISLTDIFL 113 >gnl|CDD|32729 COG2905, COG2905, Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]. Length = 610 Score = 35.6 bits (82), Expect = 0.017 Identities = 16/71 (22%), Positives = 37/71 (52%), Gaps = 7/71 (9%) Query: 101 AVEDKATVYEAMLMFEKYGRSWMPVYKNSLDNPRGMVHMRDVISYISHMYAKTNNINLNI 160 +V+ ++EAMLM + +PV ++ P G++ + D++ S N+I L Sbjct: 226 SVDRGDFLFEAMLMMLRNRIKHLPVTEDG--QPLGILTLTDILRLFSQ-----NSIVLVK 278 Query: 161 QLSESNLIKNI 171 +++ ++ I+ + Sbjct: 279 RIARASSIEEL 289 >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 = 35.3 bits (81), Expect = 0.025 Identities = 13/53 (24%), Positives = 26/53 (49%) Query: 172 LFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIVSVLMRDITSE 224 + ++ + + + ES+ ALV+D GG G+++ D++ L D E Sbjct: 4 PVLSATTPLREAAEQLIESKHGSALVVDRDGGVVGIITLPDLLRALEADEAGE 56 >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 = 35.1 bits (81), Expect = 0.027 Identities = 20/82 (24%), Positives = 38/82 (46%) Query: 174 VPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIVSVLMRDITSEHHSKKSMIS 233 V V+D+L + AL + + G GL+ E ++ +L + KK + Sbjct: 6 VSPDTTVNDVLERFERDPDLSALAVVDDGRPVGLIMREALMELLSTPYGRALYGKKPVSE 65 Query: 234 AVSDNTFIVDARTDLEELAKII 255 + + IV+A T LEE++++ Sbjct: 66 VMDPDPLIVEADTPLEEVSRLA 87 >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 = 35.1 bits (81), Expect = 0.028 Identities = 12/57 (21%), Positives = 27/57 (47%), Gaps = 4/57 (7%) Query: 89 IDDIMISRVSINAVEDKATVYEAMLMFEKYGRSWMPVYKNSLDNPRGMVHMRDVISY 145 + ++M + + ATV+EA+L+ + G +PV + G++ D++ Sbjct: 59 VSEVMTAPPI--TIPPDATVFEALLLMLERGIHHLPVVDD--GRLVGVISATDLLRL 111 >gnl|CDD|32593 COG2524, COG2524, Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]. Length = 294 Score = 33.3 bits (76), Expect = 0.090 Identities = 32/150 (21%), Positives = 71/150 (47%), Gaps = 15/150 (10%) Query: 71 SETEKEIFNNILRFR---KIRIDDIMISRVSINAVEDKATVYEAMLMFEKYGRSWMPVYK 127 +T EI +I + K ++ ++M ++ V T+ EA +F + G PV Sbjct: 153 DDTANEILIDISKMVSIPKEKVKNLMSKKLI--TVRPDDTLREAAKLFYEKGIRGAPVVD 210 Query: 128 NSLDNPRGMVHMRDVISYISHMYAKTNNINLNIQLSESNLIKNILFVPSSMLVSDLLTNI 187 + D G++ + D+ I+ N NL+ ++S+ + KN++ + + D + + Sbjct: 211 D--DKIVGIITLSDIAKAIA-------NGNLDAKVSDY-MRKNVITINEDEDIYDAIRLM 260 Query: 188 QESRIRMALVIDEHGGTDGLVSYEDIVSVL 217 ++ + LV D +G G+++ DI++ + Sbjct: 261 NKNNVGRLLVTDSNGKPVGIITRTDILTRI 290 >gnl|CDD|33866 COG4109, COG4109, Predicted transcriptional regulator containing CBS domains [Transcription]. Length = 432 Score = 33.3 bits (76), Expect = 0.097 Identities = 37/173 (21%), Positives = 77/173 (44%), Gaps = 13/173 (7%) Query: 47 KLMKLSHHKGIRLPRIDASLEGIFSETEKEIFNNILRFRKIRIDDIMISRVSINAVEDKA 106 +++KL++ KG+ + + + K + N +++ I ++DIM + + + Sbjct: 148 EVIKLANEKGLPVLSTSYDTFTVATMINKALSNQLIKKDIITVEDIMTPLEDTSYLRETD 207 Query: 107 TVYEAMLMFEKYGRSWMPVYKNSLDNPRGMVHMRDVISYISHMYAKTNNINLNIQLSESN 166 TV + + + EK G S PV N G+V MRDV+ K + + ++ Sbjct: 208 TVEDWLDLVEKTGHSRFPVV-NRSMKVVGVVTMRDVLD-------KKPSTTIEKVMT--- 256 Query: 167 LIKNILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIVSVLMR 219 KN + V + V+ + + I M V+D + G+++ +D++ L Sbjct: 257 --KNPITVRAKTSVASVAQMMIWEGIEMLPVVDSNNTLLGIITRQDVLKSLQM 307 >gnl|CDD|33251 COG3448, COG3448, CBS-domain-containing membrane protein [Signal transduction mechanisms]. Length = 382 Score = 32.7 bits (74), Expect = 0.12 Identities = 36/163 (22%), Positives = 68/163 (41%), Gaps = 22/163 (13%) Query: 66 LEGIFSETEKEIFNNILRFRKIRIDDIMISRVSINAVEDKATVYEAMLMFEKYGRSWMPV 125 LE + ETE + R ++ DIM SR + D ++ A + +++ +PV Sbjct: 226 LERLLRETELQAL--RRRMGELTCADIM-SRDVVTVSTD-TSIDHARKLLQEHRIKALPV 281 Query: 126 YKNSLDNPR---GMVHMRDVISYISHMYAKTNNINLNIQLSESNLIKNILFVPSSMLVSD 182 LD R G+V RD++ + + ++ +K I+ P + D Sbjct: 282 ----LDEHRRLVGIVTQRDLLKHARPSPFQ------RLRFLRPPTVKGIMTTPVVTVRPD 331 Query: 183 -----LLTNIQESRIRMALVIDEHGGTDGLVSYEDIVSVLMRD 220 L+ + + + V+D G G+VS D+++ L R+ Sbjct: 332 TPAVELVPRLADEGLHALPVLDAAGKLVGIVSQTDLIAALYRN 374 >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 = 31.7 bits (72), Expect = 0.27 Identities = 10/60 (16%), Positives = 27/60 (45%) Query: 174 VPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIVSVLMRDITSEHHSKKSMIS 233 +P+ + + L + + +R+ LV+D G+++ D++ E +S ++ Sbjct: 6 IPADTSIDEALELMIKHGVRLLLVVDSDDNFIGVITAVDLLGEEPIKRIQEGGISRSELT 65 >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 = 31.3 bits (71), Expect = 0.36 Identities = 14/45 (31%), Positives = 25/45 (55%) Query: 171 ILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIVS 215 +L VP+ + D ++E IR +V+D+ G GL+S D++ Sbjct: 66 LLTVPADTSLYDARQLMREHGIRHLVVVDDDGELLGLLSQTDLLQ 110 >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 = 30.9 bits (70), Expect = 0.46 Identities = 19/114 (16%), Positives = 47/114 (41%), Gaps = 10/114 (8%) Query: 101 AVEDKATVYEAMLMFEKYGRSWMPVYKNSLDNPRGMVHMRDVISYISHMYAKTNNINLNI 160 + AT+ EA +F + PV + G+V + D+ I+ Sbjct: 5 TLNPNATLREAARLFNTHHIHGAPVVDD--GKLVGIVTLSDIAHAIA-------RGLELA 55 Query: 161 QLSESNLIKNILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIV 214 ++ + + K+++ + + D + + + + +V D+ G G+++ DI+ Sbjct: 56 KVKDV-MTKDVITIDEDEQLYDAIRLMNKHNVGRLIVTDDEGRPVGIITRTDIL 108 >gnl|CDD|30863 COG0517, COG0517, FOG: CBS domain [General function prediction only]. Length = 117 Score = 30.5 bits (68), Expect = 0.69 Identities = 28/128 (21%), Positives = 59/128 (46%), Gaps = 13/128 (10%) Query: 89 IDDIMISRVSINAVEDKATVYEAMLMFEKYGRSWMPVYKNSLDNPRGMVHMRDVISYISH 148 + DIM V V+ +V +A+L+ + G S +PV + G++ RD++ ++ Sbjct: 1 VKDIMTKDVIT--VKPDTSVRDALLLMSENGVSAVPVVDD--GKLVGIITERDILRALAA 56 Query: 149 MYAKTNNINLNIQLSESNLIKNILFVPSSMLVSDLLTNIQES-RIRMALVIDEHGGT-DG 206 + + + + K ++ V + + L + E +IR V+D+ GG G Sbjct: 57 GGKRLLPV-------KEVMTKPVVTVDPDTPLEEALELMVERHKIRRLPVVDDDGGKLVG 109 Query: 207 LVSYEDIV 214 +++ DI+ Sbjct: 110 IITLSDIL 117 Score = 29.7 bits (66), Expect = 1.1 Identities = 21/98 (21%), Positives = 44/98 (44%), Gaps = 4/98 (4%) Query: 48 LMKLSHHKGIRLPRIDAS-LEGIFSETEKEIFNNILRFRKIRIDDIMISRVSINAVEDKA 106 L+ +S + +P +D L GI TE++I + K + + + V+ Sbjct: 22 LLLMSENGVSAVPVVDDGKLVGII--TERDILRALAAGGKRLLPVKEVMTKPVVTVDPDT 79 Query: 107 TVYEAM-LMFEKYGRSWMPVYKNSLDNPRGMVHMRDVI 143 + EA+ LM E++ +PV + G++ + D++ Sbjct: 80 PLEEALELMVERHKIRRLPVVDDDGGKLVGIITLSDIL 117 >gnl|CDD|37390 KOG2179, KOG2179, KOG2179, Nucleotide excision repair complex XPC-HR23B, subunit XPC/DPB11 [Replication, recombination and repair]. Length = 669 Score = 30.0 bits (67), Expect = 0.99 Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 6/79 (7%) Query: 3 SDFKINSSEHPKEKNEGIDLSPSISKTSVPAFWTRTIRALCKTWKLMKLSHHKGIR---- 58 ++N+ K K PS S+ S AF ++ R L+ LS + IR Sbjct: 112 DPVRLNALVRSKPKKIRKSFKPSSSRKS-QAFKNKSRRKTLHGLVLVCLSKYGKIRTNFL 170 Query: 59 -LPRIDASLEGIFSETEKE 76 D E + SE+E + Sbjct: 171 RKNYADLKNENLISESELK 189 >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 = 29.4 bits (66), Expect = 1.3 Identities = 25/96 (26%), Positives = 44/96 (45%), Gaps = 7/96 (7%) Query: 187 IQESRIRMALVIDEHGGTDGLVSYEDIVSVLMRDITS--EHHSKKSMISAVSD----NTF 240 ++E RIR V++E G GL++ D++ + ++ E K V++ + Sbjct: 19 MREHRIRHLPVVNEDGKLVGLLTQRDLLRAALSSLSDNGEESLTKERDVPVAEVMKTDVL 78 Query: 241 IVDARTDLEELAKIIGTD-CNCLKGEQDVDSLGGLI 275 V T L E A+I+ + CL D +L G+I Sbjct: 79 TVTPDTPLREAAEIMVENKIGCLPVVDDKGTLVGII 114 >gnl|CDD|143594 cd07570, GAT_Gln-NAD-synth, Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases). Glutamine-dependent NAD synthetases are bifunctional enzymes, which have an N-terminal GAT domain and a C-terminal NAD+ synthetase domain. The GAT domain is a glutaminase (EC 3.5.1.2) which hydrolyses L-glutamine to L-glutamate and ammonia. The ammonia is used by the NAD+ synthetase domain in the ATP-dependent amidation of nicotinic acid adenine dinucleotide. Glutamine aminotransferases are categorized depending on their active site residues into different unrelated classes. This class of GAT domain belongs to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), this subgroup corresponds to classes 7 and 8. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. Mycobacterium tuberculosis glutamine-dependent NAD+ synthetase forms a homooctamer. Length = 261 Score = 29.4 bits (67), Expect = 1.6 Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 7/44 (15%) Query: 274 LIFS----VLDRIPARGEVVLEIPGFEIVILDADVRCVRRVRIR 313 L+F + D GE++ E P FE + D D+ +R R R Sbjct: 209 LVFDGGSFIAD---NDGELLAEAPRFEEDLADVDLDRLRSERRR 249 >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 = 29.3 bits (66), Expect = 1.6 Identities = 24/113 (21%), Positives = 49/113 (43%), Gaps = 7/113 (6%) Query: 102 VEDKATVYEAMLMFEKYGRSWMPVYKNSLDNPRGMVHMRDVISYISHMYAKTNNINLNIQ 161 V T+ EA + ++ +PV +N D G+V RD++ + A + + Sbjct: 6 VSPDDTIREAARLMREHDVGALPVCEN--DRLVGIVTDRDIV-----VRAVAEGRDPDTT 58 Query: 162 LSESNLIKNILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIV 214 + + ++ V V + ++E ++R V+D+ G G+VS D+ Sbjct: 59 TVGDVMTRGVVTVTEDDDVDEAARLMREHQVRRLPVVDDDGRLVGIVSLGDLA 111 >gnl|CDD|72966 cd04494, BRCA2DBD_OB2, BRCA2DBD_OB2: A subfamily of OB folds corresponding to the second OB fold (OB2) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA).. Length = 251 Score = 28.4 bits (63), Expect = 2.5 Identities = 13/52 (25%), Positives = 25/52 (48%) Query: 61 RIDASLEGIFSETEKEIFNNILRFRKIRIDDIMISRVSINAVEDKATVYEAM 112 R LE +FS+ ++E + R +R ++ ++D A +YEA+ Sbjct: 54 RQQKKLEALFSKIQEEFEKEEEDNNQRRPRSRTRTRQNVTDLQDGAELYEAL 105 >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 = 28.6 bits (64), Expect = 2.6 Identities = 20/108 (18%), Positives = 40/108 (37%), Gaps = 7/108 (6%) Query: 107 TVYEAMLMFEKYGRSWMPVYKNSLDNPRGMVHMRDVISYISHMYAKTNNINLNIQLSESN 166 TV EA + + S + V + G+ +D+ + ++ L E Sbjct: 11 TVQEAAKLMREKRVSCVLVMDG--NKLVGIFTSKDIA-----LRVVAQGLDPESTLVERV 63 Query: 167 LIKNILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIV 214 + N + S V + L + + + R V+D+ G GL+ + Sbjct: 64 MTPNPVCATSDTPVLEALHLMVQGKFRHLPVVDKSGQVVGLLDVTKLT 111 >gnl|CDD|37329 KOG2118, KOG2118, KOG2118, Predicted membrane protein, contains two CBS domains [Function unknown]. Length = 498 Score = 28.1 bits (62), Expect = 3.2 Identities = 32/152 (21%), Positives = 66/152 (43%), Gaps = 9/152 (5%) Query: 74 EKEIFNNILRFRKIRIDDIMISRVSINAVEDKAT-VYEAMLMFEKYGRSWMPVYKNSLDN 132 E I L + + ++M + A++ E + K+G S +PVY+ N Sbjct: 191 ELTIITGALELTEKLVGEVMTPIEDVFALDANTKLDRETVGEIVKHGYSRIPVYEQEPKN 250 Query: 133 PRGMVHMRDVISYISHMYAKTNNINLNIQLSESNLIKNILFVPSSMLVSDLLTNIQESRI 192 G + + +++ + + + +SES L + VP +M + DLL Q+ + Sbjct: 251 KIGGLLVMNLLRLL----QVEVPLE-PLPVSESAL-LRLPLVPENMPLLDLLNEFQKGKS 304 Query: 193 RMALVIDEHGGTDGLVSYEDIVSVLMRDITSE 224 MA+V + H D V + + +++++ E Sbjct: 305 HMAVVRNGHV--DIFVLTLEDLEEVVKEVEDE 334 >gnl|CDD|173670 cd05579, STKc_MAST_like, Catalytic domain of Microtubule-associated serine/threonine kinase-like proteins. Serine/Threonine Kinases (STKs), Microtubule-associated serine/threonine (MAST) kinase subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MAST kinase subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. The MAST kinase subfamily includes MAST kinases, MAST-like (MASTL) kinases, and fungal kinases with similarity to Saccharomyces cerevisiae Rim15 and Schizosaccharomyces pombe cek1. MAST kinases contain an N-terminal domain of unknown function, a central catalytic domain, and a C-terminal PDZ domain that mediates protein-protein interactions. MASTL kinases carry only a catalytic domain which contains a long insert relative to other kinases. The fungal kinases in this subfamily harbor other domains in addition to a central catalytic domain, which also contains an insert relative to MAST kinases like MASTL. Rim15 contains a C-terminal signal receiver (REC) domain while cek1 contains an N-terminal PAS domain. MAST kinases are cytoskeletal associated kinases of unknown function that are also expressed at neuromuscular junctions and postsynaptic densities. The fungal proteins Rim15 and cek1 are involved in the regulation of meiosis and mitosis, respectively. Length = 265 Score = 28.0 bits (63), Expect = 3.2 Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 3/42 (7%) Query: 66 LEGI---FSETEKEIFNNILRFRKIRIDDIMISRVSINAVED 104 L GI ET +EIF NIL + +D+ +S +I+ + Sbjct: 195 LVGIPPFHGETPEEIFQNILNGKIEWPEDVEVSDEAIDLISK 236 >gnl|CDD|30495 COG0146, HyuB, N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]. Length = 563 Score = 28.3 bits (63), Expect = 3.2 Identities = 18/96 (18%), Positives = 35/96 (36%), Gaps = 8/96 (8%) Query: 53 HHKGIRLPRIDASLEGIFSETEKEIFNNILRFRKIRIDDIMISRVSINAVEDKATVYEAM 112 +G+R+P + G F E I +R I D+ ++++ N Sbjct: 144 FQEGLRIPPVKLVKNGEFREDILRILLRNVRTPDYNIGDLK-AQIAAN----LKGRRRVR 198 Query: 113 LMFEKYGR-SWMPVYKNSLDNPRGMVHMRDVISYIS 147 + ++YG + K ++ V R VI + Sbjct: 199 ELIDEYGLDTVEEAMKEVIEYAERAV--RAVIRKLP 232 >gnl|CDD|38870 KOG3666, KOG3666, KOG3666, Uncharacterized conserved protein [Function unknown]. Length = 1141 Score = 28.1 bits (62), Expect = 3.4 Identities = 13/64 (20%), Positives = 27/64 (42%), Gaps = 4/64 (6%) Query: 72 ETEKEIFNNILRFRKIRIDDIMIS---RVSINAVED-KATVYEAMLMFEKYGRSWMPVYK 127 KE+ N + F+KI + D + + +NAV K+ V + ++ ++ Sbjct: 868 MLVKELQNFLSMFQKIILSDRTVQDTLKTLMNAVSPLKSIVANSNKIYFSAIAKTQKIWT 927 Query: 128 NSLD 131 L+ Sbjct: 928 ALLE 931 >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 = 28.1 bits (63), Expect = 3.6 Identities = 30/113 (26%), Positives = 53/113 (46%), Gaps = 11/113 (9%) Query: 102 VEDKATVYEAMLMFEKYGRSWMPVYKNSLDNPRGMVHMRDVISYISHMYAKTNNINLNIQ 161 V ATV EA+ + +YG S +PV + G+V RD + + + +L+ Sbjct: 7 VSPDATVAEALELMAEYGISGLPVVDDD-GKLVGIVTNRD-LRFET---------DLDKP 55 Query: 162 LSESNLIKNILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIV 214 +SE +N+L + + L + E +I V+D+ G GL++ +DI Sbjct: 56 VSEVMTPENLLTTVEGTSLEEALELLHEHKIEKLPVVDDEGKLKGLITVKDIE 108 >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 = 27.9 bits (62), Expect = 3.8 Identities = 19/129 (14%), Positives = 52/129 (40%), Gaps = 14/129 (10%) Query: 98 SINAVEDKATVYEAMLMFEKYGRSWMPVYKNSLDNPRGMVH---MRDV-------ISYIS 147 + +++ V +A + K S +PV +D ++ D+ + Sbjct: 2 KVVSIDSDERVLDAFKLMRKNNISGLPV----VDEKGKLIGNISASDLKGLLLSPDDLLL 57 Query: 148 HMYAKTNNINLNIQLSESNLIKNILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGL 207 + ++ S+ + ++ S + +++T + +++ V+DE G G+ Sbjct: 58 YRTITFKELSEKFTDSDGVKSRPLITCTPSSTLKEVITKLVANKVHRVWVVDEEGKPIGV 117 Query: 208 VSYEDIVSV 216 ++ DI+S+ Sbjct: 118 ITLTDIISI 126 >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 = 27.6 bits (62), Expect = 4.4 Identities = 32/163 (19%), Positives = 58/163 (35%), Gaps = 30/163 (18%) Query: 88 RIDDIMISRVSINAVEDKATVYEAMLMFEKYGRSWMPVYKNS-----LDNPRGMVHMRDV 142 R + I+ V TV EA+ + E+YG S +PV ++ L R + + Sbjct: 83 RFESGFITDPVT--VSPDTTVAEALELKERYGISGVPVTEDGKLLGGLVGIRTSRDIDFL 140 Query: 143 ISYISHMYAKTNNINL--NIQLSESNLIKNILFVPSSMLVSDLLTNIQESRIRMALVIDE 200 M + + I L E+N I + E +I ++D+ Sbjct: 141 SKVSVVMTMTEDLVTAPEGITLEEANEI------------------LHEHKIEKLPIVDD 182 Query: 201 HGGTDGLVSYEDIVSVLMRDITSEHHSKKSMISA---VSDNTF 240 G GL++ +DI S+ + ++ A D+ Sbjct: 183 DGELVGLITRKDIEKARDYPNASKDAQGRLLVGAAVGTRDDDL 225 >gnl|CDD|144473 pfam00888, Cullin, Cullin family. Length = 605 Score = 27.6 bits (61), Expect = 5.0 Identities = 29/139 (20%), Positives = 54/139 (38%), Gaps = 13/139 (9%) Query: 125 VYKNSLDNPRGMVHMRDVISYISHMYAKTNNINLNIQLSESNLIKNILFVPSSMLVSDLL 184 YK M + ++ Y++ Y K + +L +++ L+ LL Sbjct: 73 YYKEWNKFSTSMKILNNIFMYLNRYYVKRKEVYEIYELGLDIWRESLFDPIKDKLIDALL 132 Query: 185 TNIQESR---------IRMALVIDEHGGTDGLVSYEDIVSVLMRDITSEHHSKKSMI--- 232 I++ R I+ L + G D L Y++ + TSE + K+S Sbjct: 133 RLIEKERLGEIIDRSLIKNVLDMFVELGDDSLSVYKEDFEKPFLEATSEFYKKESSKFLQ 192 Query: 233 -SAVSDNTFIVDARTDLEE 250 ++VS+ V+ R + EE Sbjct: 193 ENSVSEYMKKVEERLEEEE 211 >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 = 27.4 bits (61), Expect = 5.5 Identities = 20/111 (18%), Positives = 44/111 (39%), Gaps = 13/111 (11%) Query: 106 ATVYEAMLMFEKYGRSWMPVYKNSLDNPRGMVHMRDVISYISHMYAKTNNINLNIQLSES 165 + E M +YG S +PV + G + D++ + +L + Sbjct: 13 SQAIERM---REYGVSQLPVVDD--GRVVGSIDESDLLD---ALIEGKAKFSLPV---RE 61 Query: 166 NLIKNILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIVSV 216 + + + V + +L + R +A+V+DE G G+++ D++ Sbjct: 62 VMGEPLPTVDPDAPIEELSELLD--RGNVAVVVDEGGKFVGIITRADLLKY 110 >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 = 27.5 bits (61), Expect = 5.5 Identities = 30/114 (26%), Positives = 58/114 (50%), Gaps = 10/114 (8%) Query: 102 VEDKATVYE-AMLMFEKYGRSWMPVYKNSLDNPRGMVHMRDVISYISHMYAKTNNINLNI 160 V+ ++ E A LM E+ S V + + P G+V RD++ A I+L+ Sbjct: 6 VDPDTSIREAAKLMAEENVGS--VVVVDPDERPIGIVTERDIV------RAVAAGIDLDT 57 Query: 161 QLSESNLIKNILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIV 214 +SE + ++++ V V++ ++++ IR LV+D+ G G++S D+V Sbjct: 58 PVSEI-MTRDLVTVDPDEPVAEAAKLMRKNNIRHHLVVDKGGELVGVISIRDLV 110 >gnl|CDD|99790 cd06193, siderophore_interacting, Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from transferrin and lactoferrin for bacterial uptake, contributing to pathogen virulence. Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in a variety of organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one-electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and two electron carriers. FNR has a strong preference for NADP(H) vs NAD(H).. Length = 235 Score = 27.2 bits (61), Expect = 5.6 Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 7/42 (16%) Query: 275 IFSVLDRIP--ARGEVVLEIPG-FEIVILDA----DVRCVRR 309 I ++L+ +P ARG ++E+P + L A +V + R Sbjct: 135 IAAILEELPADARGTALIEVPDAADEQPLPAPAGVEVTWLHR 176 >gnl|CDD|36589 KOG1375, KOG1375, KOG1375, Beta tubulin [Cytoskeleton]. Length = 369 Score = 27.4 bits (60), Expect = 5.6 Identities = 11/24 (45%), Positives = 17/24 (70%) Query: 250 ELAKIIGTDCNCLKGEQDVDSLGG 273 E A+++ + C+CL+G Q SLGG Sbjct: 63 EGAELVDSSCDCLQGFQLTHSLGG 86 >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 = 27.0 bits (60), Expect = 6.3 Identities = 18/87 (20%), Positives = 37/87 (42%), Gaps = 2/87 (2%) Query: 169 KNILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIVSVLMRDITSEHHSK 228 ++++ V V++ + E I +V+D+ G G+ S DIV + S + Sbjct: 1 RDVITVRPDATVAEAAKLMAEKNIGAVVVVDDGGRLVGIFSERDIVRKVALRGASALDTP 60 Query: 229 KSMISAVSDNTFIVDARTDLEELAKII 255 S I ++ N V ++E ++ Sbjct: 61 VSEI--MTRNVITVTPDDTVDEAMALM 85 >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 = 27.0 bits (60), Expect = 7.5 Identities = 9/43 (20%), Positives = 23/43 (53%) Query: 174 VPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIVSV 216 + L ++ L ++E++I V+D++G G++ D++ Sbjct: 72 IDPDALAAEALELMEENKITALPVVDDNGRPVGVLHIHDLLRA 114 >gnl|CDD|36975 KOG1764, KOG1764, KOG1764, 5'-AMP-activated protein kinase, gamma subunit [Energy production and conversion]. Length = 381 Score = 26.9 bits (59), Expect = 7.6 Identities = 36/184 (19%), Positives = 71/184 (38%), Gaps = 14/184 (7%) Query: 47 KLMKLSHHKGIRLPRID---ASLEGIFSETE--KEIFNNILRFRKIRIDDIMISRVSINA 101 ++ L + R+P ID + I ++ K ++ N + +S + I Sbjct: 176 AVLLLIKSRIHRVPVIDPETGEVLYILTQRRILKFLWLNGRLLPLPSLLSKSLSDLGIGT 235 Query: 102 VEDKA------TVYEAMLMFEKYGRSWMPVYKNSLDNPRGMVHMRDVISYI-SHMYAKTN 154 + A V EA+ + + S +PV + G DVI Y + Sbjct: 236 WSNIASISEDTPVIEALKIMSERRISALPVV-DENGKKVGNYSRFDVIHLAREGTYNNLD 294 Query: 155 NINLNIQLSESNLIKN-ILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDI 213 L+ LS + ++ + +++++ + R+ V+DE G G++S DI Sbjct: 295 LSCLSEALSHRPIRFEGVVTCRPTSTLAEVIDKLVAHRVHRLWVVDEDGVLVGVISLSDI 354 Query: 214 VSVL 217 +S L Sbjct: 355 LSYL 358 >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 = 27.0 bits (60), Expect = 7.7 Identities = 23/88 (26%), Positives = 44/88 (50%), Gaps = 7/88 (7%) Query: 168 IKNILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIVSVLMRDITSEHHS 227 IK +L P + ++ D L I ++ +R+ LV+DE+G G V+ DI L++ ++ + Sbjct: 2 IKQLLVSPDASIL-DALRKIDKNALRIVLVVDENGRLLGTVTDGDIRRALLKGLSLD--- 57 Query: 228 KKSMISAVSDNTFIV-DARTDLEELAKI 254 +S V + I + EE+ + Sbjct: 58 --DPVSEVMNRNPITAKVGSSREEILAL 83 >gnl|CDD|176919 cd08910, START_STARD2-like, Lipid-binding START domain of mammalian STARD2 and related proteins. This subgroup includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of STARD2 (also known as phosphatidylcholine transfer protein/PC-TP) and related proteins. It belongs to the START domain family, and in turn to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. STARD2 is a cytosolic phosphatidycholine (PtdCho) transfer protein, which traffics PtdCho, the most common class of phospholipids in eukaryotes, between membranes. It represents a minimal START domain structure. STARD2 plays roles in hepatic cholesterol metabolism, in the development of atherosclerosis, and may have a mitochondrial function. Length = 207 Score = 26.7 bits (59), Expect = 7.9 Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 12/77 (15%) Query: 82 LRFRKIRIDDIMISRVSINAVEDKATV-----YEAMLMFEKYGRSWMPVYKNSLDNPRGM 136 + RKI + I+ S+ + +K V Y+ L E G+ V+ DNP GM Sbjct: 122 VEGRKIWV--ILARSTSLPQLPEKPGVIRVKQYKQSLAIESDGKKGSKVFMYYFDNPGGM 179 Query: 137 VHMRDVISYISHMYAKT 153 + S++ + AK Sbjct: 180 IP-----SWLINWAAKN 191 >gnl|CDD|36229 KOG1011, KOG1011, KOG1011, Neurotransmitter release regulator, UNC-13 [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport]. Length = 1283 Score = 26.6 bits (58), Expect = 8.6 Identities = 21/102 (20%), Positives = 44/102 (43%), Gaps = 8/102 (7%) Query: 183 LLTNIQESRIRMALVIDEHGGTDGLVSYEDIVSVLMRDITSEHHSKKSMISAVSDNTFIV 242 L+ N+Q+ R+++ + + GG + D++ L + +S +SAV +F Sbjct: 850 LMNNVQQLRVQLEKMFEAMGGKELDEEAGDVLKELQVKL----NSVLDELSAVFVTSFQP 905 Query: 243 DARTDLEELAKII----GTDCNCLKGEQDVDSLGGLIFSVLD 280 + ++ I+ GT QD D++ + +LD Sbjct: 906 HIHECVIQMGDILVQVKGTGLAKTSVAQDADAVLEPLMDLLD 947 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 0.321 0.136 0.389 Gapped Lambda K H 0.267 0.0582 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,790,637 Number of extensions: 198681 Number of successful extensions: 521 Number of sequences better than 10.0: 1 Number of HSP's gapped: 496 Number of HSP's successfully gapped: 71 Length of query: 320 Length of database: 6,263,737 Length adjustment: 94 Effective length of query: 226 Effective length of database: 4,232,491 Effective search space: 956542966 Effective search space used: 956542966 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: 57 (26.1 bits)