RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780276|ref|YP_003064689.1| dihydrodipicolinate synthase
[Candidatus Liberibacter asiaticus str. psy62]
(292 letters)
>gnl|CDD|179547 PRK03170, PRK03170, dihydrodipicolinate synthase; Provisional.
Length = 292
Score = 409 bits (1053), Expect = e-115
Identities = 136/292 (46%), Positives = 181/292 (61%), Gaps = 3/292 (1%)
Query: 1 MFRGSIPALITPFTKGNLIDEDAFVEHIEWQITEGSGGLVPAGTTGESSTLSHEEHCRII 60
MF GSI AL+TPF + +D A + +++ I G+ GLV GTTGES TL+HEEH +I
Sbjct: 1 MFGGSITALVTPFKEDGSVDFAALRKLVDYLIANGTDGLVVVGTTGESPTLTHEEHEELI 60
Query: 61 ELCVKTVASRVPVMAGIGSNNTRESVELAQYAHSIGADALLVVIPYYNKPNRRGLLAHFG 120
V+ V RVPV+AG GSN+T E++EL ++A GAD LVV PYYNKP + GL HF
Sbjct: 61 RAVVEAVNGRVPVIAGTGSNSTAEAIELTKFAEKAGADGALVVTPYYNKPTQEGLYQHFK 120
Query: 121 EIATTVSSPIYIYNNPSRTVIEMDVDTMAELAATYPNIVGVKDATGKIELVSEQRLSCGF 180
IA PI +YN P RT +++ +T+A LA +PNIVG+K+ATG +E VSE
Sbjct: 121 AIAEATDLPIILYNVPGRTGVDILPETVARLAE-HPNIVGIKEATGDLERVSELIELVPD 179
Query: 181 DFIQLSGEDSSALGFNAHGGVGCISVTANVVPRICAEFQQAMIRGDYRQALLYQDKLMPL 240
DF SG+D+ AL F A GGVG ISV ANV P+ AE A + GD+ +A +L+PL
Sbjct: 180 DFAVYSGDDALALPFLALGGVGVISVAANVAPKEMAEMCDAALAGDFAEAREIHRRLLPL 239
Query: 241 HQALFMEPAVCCVKYALSRLGRNVSLAVRSPMVSTLEKDTMIAIDQALERLG 292
H+ALF+EP VK AL+ LG +R P+V L ++ + AL+ G
Sbjct: 240 HKALFIEPNPIPVKAALNLLGLIEG-ELRLPLV-PLSEEEKEKLRAALKEAG 289
>gnl|CDD|129757 TIGR00674, dapA, dihydrodipicolinate synthase. Dihydrodipicolinate
synthase is a homotetrameric enzyme of lysine
biosynthesis. E. coli has several paralogs closely
related to dihydrodipicoline synthase (DapA), as well as
the more distant N-acetylneuraminate lyase. In
Pyrococcus horikoshii, the bidirectional best hit with
E. coli is to an uncharacterized paralog of DapA, not
DapA itself, and it is omitted from the seed. The
putative members from the Chlamydias (pathogens with a
parasitic metabolism) are easily the most divergent
members of the multiple alignment.
Length = 285
Score = 286 bits (734), Expect = 5e-78
Identities = 127/270 (47%), Positives = 166/270 (61%), Gaps = 2/270 (0%)
Query: 4 GSIPALITPFTKGNLIDEDAFVEHIEWQITEGSGGLVPAGTTGESSTLSHEEHCRIIELC 63
G I ALITPF + +D A + I++QI G+ +V GTTGES TLSHEEH ++IE
Sbjct: 1 GVITALITPFKEDGSVDFAALEKLIDFQIENGTDAIVVVGTTGESPTLSHEEHKKVIEFV 60
Query: 64 VKTVASRVPVMAGIGSNNTRESVELAQYAHSIGADALLVVIPYYNKPNRRGLLAHFGEIA 123
V V RVPV+AG GSN T E++ L ++A +GAD LVV PYYNKP + GL HF IA
Sbjct: 61 VDLVNGRVPVIAGTGSNATEEAISLTKFAEDVGADGFLVVTPYYNKPTQEGLYQHFKAIA 120
Query: 124 TTVSSPIYIYNNPSRTVIEMDVDTMAELAATYPNIVGVKDATGKIELVSEQRLSCGFDFI 183
V PI +YN PSRT + + +T+ LA PNIV +K+ATG +E +SE + DF+
Sbjct: 121 EEVDLPIILYNVPSRTGVSLYPETVKRLAE-EPNIVAIKEATGNLERISEIKAIAPDDFV 179
Query: 184 QLSGEDSSALGFNAHGGVGCISVTANVVPRICAEFQQAMIRGDYRQALLYQDKLMPLHQA 243
LSG+D+ L A GG G ISVTANV P++ E + GD+ +A KLMPLH+A
Sbjct: 180 VLSGDDALTLPMMALGGKGVISVTANVAPKLMKEMVNNALEGDFAEAREIHQKLMPLHKA 239
Query: 244 LFMEPAVCCVKYALSRLGRNVSLAVRSPMV 273
LF+E VK AL+ LG +R P+
Sbjct: 240 LFIETNPIPVKTALALLGLIEG-ELRLPLT 268
>gnl|CDD|131366 TIGR02313, HpaI-NOT-DapA, 2,4-dihydroxyhept-2-ene-1,7-dioic acid
aldolase. This model represents a subset of the DapA
(dihydrodipicolinate synthase) family which has
apparently evolved a separate function. The product of
DapA, dihydrodipicolinate, results from the
non-enzymatic cyclization and dehydration of
6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is
different from the substrate of this reaction only in
the presence of the amino group. In the absence of this
amino group, and running the reaction in the opposite
direction, the reaction corresponds to the HpaI aldolase
component of the 4-hydroxyphenylacetic acid catabolism
pathway (see TIGR02311). At present, this variant of
DapA is found only in Oceanobacillus iheyensis HTE831
and Thermus thermophilus HB27. In both of these cases,
one or more other DapA genes can be found and the one
identified by this model is part of an operon for
4-hydroxyphenylacetic acid catabolism.
Length = 294
Score = 222 bits (567), Expect = 7e-59
Identities = 107/272 (39%), Positives = 149/272 (54%), Gaps = 2/272 (0%)
Query: 2 FRGSIPALITPFTKGNLIDEDAFVEHIEWQITEGSGGLVPAGTTGESSTLSHEEHCRIIE 61
FRGSI LITPF + IDE+A E IE+QI GS + GT+GE +L+ EE + IE
Sbjct: 1 FRGSIAPLITPFKRNGDIDEEALRELIEFQIEGGSHAISVGGTSGEPGSLTLEERKQAIE 60
Query: 62 LCVKTVASRVPVMAGIGSNNTRESVELAQYAHSIGADALLVVIPYYNKPNRRGLLAHFGE 121
+ +A R+P G G+ N E++EL ++A GADA +V++PYYNKPN+ L HF E
Sbjct: 61 NAIDQIAGRIPFAPGTGALNHDETLELTKFAEEAGADAAMVIVPYYNKPNQEALYDHFAE 120
Query: 122 IATTVSS-PIYIYNNPSRTVIEMDVDTMAELAATYPNIVGVKDATGKIELVSEQRLSCGF 180
+A V PI IYN P R E+ TMA L PNIVG K++ E ++ L G
Sbjct: 121 VADAVPDFPIIIYNIPGRAAQEIAPKTMARLRKDCPNIVGAKESNKDFEHLNHLFLEAGR 180
Query: 181 DFIQLSGEDSSALGFNAHGGVGCISVTANVVPRICAEFQQAMIRGDYRQALLYQDKLMPL 240
DF+ G + L A G G I+ TANV P+ AE +A GD + A +L+
Sbjct: 181 DFLLFCGIELLCLPMLAIGAAGSIAATANVEPKEVAELCEAAEAGDIKGAQDLHFELLEA 240
Query: 241 HQALFMEPAVCCVKYALSRLGRNVSLAVRSPM 272
+ A+F + +K AL +G + +R P+
Sbjct: 241 NDAIFKDTNPAPLKAALGMMGL-IEKELRPPL 271
>gnl|CDD|178038 PLN02417, PLN02417, dihydrodipicolinate synthase.
Length = 280
Score = 191 bits (488), Expect = 2e-49
Identities = 88/292 (30%), Positives = 141/292 (48%), Gaps = 20/292 (6%)
Query: 4 GSIPALITPFTKGNLIDEDAFVEHIEWQITEGSGGLVPAGTTGESSTLSHEEHCRIIELC 63
I A+ TP+ D +A+ + QI G+ GL+ GTTGE +S +EH +I
Sbjct: 4 RLITAIKTPYLPDGRFDLEAYDSLVNMQIENGAEGLIVGGTTGEGQLMSWDEHIMLIGHT 63
Query: 64 VKTVASRVPVMAGIGSNNTRESVELAQYAHSIGADALLVVIPYYNKPNRRGLLAHFGEIA 123
V ++ V+ GSN+TRE++ + ++G A L + PYY K ++ GL+ HF +
Sbjct: 64 VNCFGGKIKVIGNTGSNSTREAIHATEQGFAVGMHAALHINPYYGKTSQEGLIKHFETVL 123
Query: 124 TTVSSPIYIYNNPSRTVIEMDVDTMAELAATYPNIVGVKDATG--KIELVSEQRLSCGFD 181
P IYN P RT ++ + + ++A +PN GVK+ TG +++ +E+ +
Sbjct: 124 DM--GPTIIYNVPGRTGQDIPPEVIFKIAQ-HPNFAGVKECTGNDRVKQYTEKGILL--- 177
Query: 182 FIQLSGEDSSALGFN-AHGGVGCISVTANVVPRICAEFQQAMIRGDYRQALLYQDKLMPL 240
SG D +G G ISVT+N+VP + + M G + L DKL+PL
Sbjct: 178 ---WSGNDDECHDARWDYGADGVISVTSNLVPGL---MHKLMFAG--KNKEL-NDKLLPL 228
Query: 241 HQALFMEPAVCCVKYALSRLGRNVSLAVRSPMVSTLEKDTMIAIDQALERLG 292
LF EP + AL++LG + R P V L+ ++ +G
Sbjct: 229 MDWLFCEPNPIGLNTALAQLGL-IRPVFRLPYVP-LDLAKRAEFVALVKAIG 278
>gnl|CDD|179610 PRK03620, PRK03620, 5-dehydro-4-deoxyglucarate dehydratase;
Provisional.
Length = 303
Score = 150 bits (382), Expect = 3e-37
Identities = 90/291 (30%), Positives = 139/291 (47%), Gaps = 16/291 (5%)
Query: 10 ITPFTKGNLIDEDAFVEHIEWQITEGSGGLVPAGTTGESSTLSHEEHCRIIELCVKTVAS 69
+TPF DE A+ EH+EW G+ L AG TGE +L+ +E+ +++ V+T A
Sbjct: 16 VTPFDADGSFDEAAYREHLEWLAPYGAAALFAAGGTGEFFSLTPDEYSQVVRAAVETTAG 75
Query: 70 RVPVMAGIGSNNTRESVELAQYAHSIGADALLVVIPYYNKPNRRGLLAHFGEIATTVSSP 129
RVPV+AG G T +++E AQ A GAD +L++ PY + + GL AH + +
Sbjct: 76 RVPVIAGAGG-GTAQAIEYAQAAERAGADGILLLPPYLTEAPQEGLAAHVEAVCKSTDLG 134
Query: 130 IYIYNNPSRTVIEMDVDTMAELAATYPNIVGVKDATGKIELVSEQRLSCGFDFIQLSGED 189
+ +YN R + DT+A LA PN+VG KD G IEL+ + G + L G
Sbjct: 135 VIVYN---RDNAVLTADTLARLAERCPNLVGFKDGVGDIELMQRIVRALGDRLLYLGGLP 191
Query: 190 SSALGFNAHGGVGCI---SVTANVVPRICAEFQQAMIRGDYRQAL---LYQDKLMPLHQA 243
++ + A+ +G S N VP I F +A+ GD A L D +P
Sbjct: 192 TAEVFAAAYLALGVPTYSSAVFNFVPEIALAFYRALRAGD--HATVDRLLDDFFLPYVAL 249
Query: 244 LFMEP--AVCCVKYALSRLGRNVSLAVRSPMVSTLEKDTMIAIDQALERLG 292
+ AV VK +G + VR+P+ L + + + + + G
Sbjct: 250 RNRKKGYAVSIVKAGARLVGLDAG-PVRAPLTD-LTPEELAELAALIAKGG 298
>gnl|CDD|132293 TIGR03249, KdgD, 5-dehydro-4-deoxyglucarate dehydratase.
5-dehydro-4-deoxyglucarate dehydratase not only
catalyzes the dehydration of the substrate (diol to
ketone + water), but causes the decarboxylation of the
intermediate product to yield 2-oxoglutarate
semialdehyde (2,5-dioxopentanoate). The gene for the
enzyme is usually observed in the vicinity of
transporters and dehydratases handling D-galactarate and
D-gluconate as well as aldehyde dehydrogenases which
convert the product to alpha-ketoglutarate.
Length = 296
Score = 137 bits (346), Expect = 5e-33
Identities = 84/289 (29%), Positives = 140/289 (48%), Gaps = 12/289 (4%)
Query: 10 ITPFTKGNLIDEDAFVEHIEWQITEGSGGLVPAGTTGESSTLSHEEHCRIIELCVKTVAS 69
+TPF DE A+ E+IEW + G L AG TGE +L+ E+ +++E+ V T
Sbjct: 14 VTPFDADGSFDEAAYRENIEWLLGYGLEALFAAGGTGEFFSLTPAEYEQVVEIAVSTAKG 73
Query: 70 RVPVMAGIGSNNTRESVELAQYAHSIGADALLVVIPYYNKPNRRGLLAHFGEIATTVSSP 129
+VPV G+G NT +++E+A+ A GAD L++ PY + GL AH + +
Sbjct: 74 KVPVYTGVGG-NTSDAIEIARLAEKAGADGYLLLPPYLINGEQEGLYAHVEAVCESTDLG 132
Query: 130 IYIYNNPSRTVIEMDVDTMAELAATYPNIVGVKDATGKIELVSEQRLSCGFDFIQLSG-- 187
+ +Y R ++ DT+ LA PN+VG KD G +E + E G L G
Sbjct: 133 VIVYQ---RDNAVLNADTLERLADRCPNLVGFKDGIGDMEQMIEITQRLGDRLGYLGGMP 189
Query: 188 -EDSSALGFNAHGGVGCISVTANVVPRICAEFQQAMIRGDYRQAL-LYQDKLMPLHQALF 245
+ +A + G S N +P I F +A+ RGD+ +Y++ ++P+++
Sbjct: 190 TAEVTAPAYLPLGVTSYSSAIFNFIPHIARAFYEALRRGDHATVGEIYKEFILPINEIRN 249
Query: 246 MEP--AVCCVKYALSRLGRNVSLAVRSPMVSTLEKDTMIAIDQALERLG 292
+ AV +K + +G VR P+ L K+ ++ L++ G
Sbjct: 250 RKKGYAVSIIKAGMEIVGLPAG-PVRPPLTD-LTKEEYAQLEVILKKAG 296
>gnl|CDD|179749 PRK04147, PRK04147, N-acetylneuraminate lyase; Provisional.
Length = 293
Score = 120 bits (303), Expect = 4e-28
Identities = 75/242 (30%), Positives = 119/242 (49%), Gaps = 19/242 (7%)
Query: 2 FRGSIPALITPFTKGNLIDEDAFVEHIEWQI-TEGSGGLVPAGTTGESSTLSHEEHCRII 60
+G AL+TPF + IDE + + I +G GL G+TGE+ LS EE +++
Sbjct: 4 LKGVYAALLTPFDEDGQIDEQGLRRLVRFNIEKQGIDGLYVGGSTGEAFLLSTEEKKQVL 63
Query: 61 ELCVKTVASRVPVMAGIGSNNTRESVELAQYAHSIGADALLVVIPYYNKPNRRGLLAHFG 120
E+ + +V ++A +GS NT E+ ELA+YA +G DA+ V P+Y + + ++
Sbjct: 64 EIVAEEAKGKVKLIAQVGSVNTAEAQELAKYATELGYDAISAVTPFYYPFSFEEICDYYR 123
Query: 121 EIATTVSSPIYIYNNPSRTVIEMDVDTMAELAATYPNIVGVKDATGKIELVSEQR----- 175
EI + +P+ +YN P+ T + + +D EL T P ++GVK G + + R
Sbjct: 124 EIIDSADNPMIVYNIPALTGVNLSLDQFNEL-FTLPKVIGVKQTAGDLYQLERIRKAFPD 182
Query: 176 --LSCGFDFIQLSGEDSSALGFNAHGGVGCISVTANVV-PRICAEFQQAMIRGDYRQALL 232
+ GFD + SG G + G I T NV R F +A GD ++A
Sbjct: 183 KLIYNGFDEMFASG---LLAGAD-----GAIGSTYNVNGWRARQIF-EAAKAGDIQEAQE 233
Query: 233 YQ 234
Q
Sbjct: 234 LQ 235
>gnl|CDD|129766 TIGR00683, nanA, N-acetylneuraminate lyase. N-acetylneuraminate
lyase is also known as N-acetylneuraminic acid aldolase,
sialic acid aldolase, or sialate lyase. It is an
intracellular enzyme. The structure of this
homotetrameric enzyme related to dihydrodipicolinate
synthase is known. In Clostridium tertium, the enzyme
appears to be in an operon with a secreted sialidase
that releases sialic acid from host
sialoglycoconjugates. In several E. coli strains,
however, this enzyme is responsible for
N-acetyl-D-neuraminic acid synthesis for capsule
production by condensing N-acetyl-D-mannosamine and
pyruvate.
Length = 290
Score = 98.1 bits (244), Expect = 2e-21
Identities = 75/300 (25%), Positives = 121/300 (40%), Gaps = 20/300 (6%)
Query: 2 FRGSIPALITPFTKGNLIDEDAFVEHIEWQITEGS-GGLVPAGTTGESSTLSHEEHCRII 60
+G AL+ F + I+E + I I + GL G+TGE+ LS EE I
Sbjct: 1 LKGIFSALLVSFNEDGTINEKGLRQIIRHNIDKMKVDGLYVGGSTGENFMLSTEEKKEIF 60
Query: 61 ELCVKTVASRVPVMAGIGSNNTRESVELAQYAHSIGADALLVVIPYYNKPNRRGLLAHFG 120
+ ++ ++A +GS N +E+VEL +YA +G D L V P+Y K + + ++
Sbjct: 61 RIAKDEAKDQIALIAQVGSVNLKEAVELGKYATELGYDCLSAVTPFYYKFSFPEIKHYYD 120
Query: 121 E-IATTVSSPIYIYNNPSRTVIEMDVDTMAELAATYPNIVGVKDATGKIELVSEQR---- 175
IA T + +Y+ P T + M ++ EL P ++GVK G L+ +
Sbjct: 121 TIIAETGGLNMIVYSIPFLTGVNMGIEQFGEL-YKNPKVLGVKFTAGDFYLLERLKKAYP 179
Query: 176 ---LSCGFDFIQLSGEDSSALGFNAHGGVGCISVTANVVPRICAEFQQAMIRGDYRQALL 232
+ GFD + L G +G T NV + + G ++AL
Sbjct: 180 NHLIWAGFDEMMLPA-----ASLGVDGAIGS---TFNVNGVRARQIFELTKAGKLQEALE 231
Query: 233 YQDKLMPLHQALFMEPAVCCVKYALSRLGRNVSLAVRSPMVST-LEKDTMIAIDQALERL 291
Q L + + +K L G + R PM S + A D + L
Sbjct: 232 IQHVTNDLIEGILANGLYLTIKELLKLEGVDAGYC-REPMTSKATPEQKAKAKDLKAKFL 290
>gnl|CDD|183608 PRK12582, PRK12582, acyl-CoA synthetase; Provisional.
Length = 624
Score = 30.4 bits (69), Expect = 0.51
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 50 TLSHEEHCRIIELCVKTVASRVPVMAGIGSNNT 82
TLS + + R+ L V+T R+P G G+ T
Sbjct: 357 TLSDDLYERMQALAVRTTGHRIPFYTGYGATET 389
>gnl|CDD|152388 pfam11953, DUF3470, Domain of unknown function (DUF3470). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria. This domain is about 50
amino acids in length. This domain is found associated
with pfam00037. This domain has a single completely
conserved residue N that may be functionally important.
Length = 49
Score = 29.0 bits (66), Expect = 1.4
Identities = 12/35 (34%), Positives = 15/35 (42%), Gaps = 10/35 (28%)
Query: 149 AELAATYPNIVGVKDA----------TGKIELVSE 173
AELA +PNI KD K+E +S
Sbjct: 15 AELAKKWPNITEKKDPLPDAEEWDGVPDKLEYLSR 49
>gnl|CDD|178956 PRK00278, trpC, indole-3-glycerol-phosphate synthase; Reviewed.
Length = 260
Score = 28.6 bits (65), Expect = 1.8
Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 11/72 (15%)
Query: 87 ELAQYAHSIGADALLVVIPYYNKPNRRGLLAHFGEIATTVSSPIYIYNNPSRTVIEMDVD 146
EL YAHS+G D L+ V + L E A + +P+ NN + E+D++
Sbjct: 151 ELLDYAHSLGLDVLVEV------HDEEEL-----ERALKLGAPLIGINNRNLKTFEVDLE 199
Query: 147 TMAELAATYPNI 158
T LA P+
Sbjct: 200 TTERLAPLIPSD 211
>gnl|CDD|162987 TIGR02722, lp_, uncharacterized proteobacterial lipoprotein.
Members of this protein family are restricted to the
Proteobacteria, and all are predicted lipoproteins. In
genomes that contain the thiK gene for the salvage
enzyme thiamin kinase, the member of this family is
encoded nearby.
Length = 189
Score = 28.6 bits (64), Expect = 1.8
Identities = 10/38 (26%), Positives = 16/38 (42%)
Query: 135 NPSRTVIEMDVDTMAELAATYPNIVGVKDATGKIELVS 172
S T +E +TM + + P + + T I LV
Sbjct: 38 GFSSTDLEPIANTMPQSMLSSPAVAQITPGTRPILLVD 75
>gnl|CDD|171118 PRK11449, PRK11449, putative deoxyribonuclease YjjV; Provisional.
Length = 258
Score = 28.0 bits (62), Expect = 2.8
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 13/73 (17%)
Query: 178 CGFDFIQLSGEDSSALGFNAHGGVGCISVTANVVPRICAEFQQAMIRGDYRQALLYQDKL 237
C FDF SG++ ++L A GVG I +VP AE ++ + L ++
Sbjct: 10 CHFDFPPFSGDEEASLQRAAQAGVGKI-----IVPATEAE--------NFARVLALAERY 56
Query: 238 MPLHQALFMEPAV 250
PL+ AL + P +
Sbjct: 57 QPLYAALGLHPGM 69
>gnl|CDD|169554 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau;
Validated.
Length = 709
Score = 28.1 bits (62), Expect = 2.8
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 6/53 (11%)
Query: 50 TLSHEEHCRIIELCVKTVASR------VPVMAGIGSNNTRESVELAQYAHSIG 96
H E C + + C + A R + + G +N RE +E AQYA + G
Sbjct: 66 NAQHGEPCGVCQSCTQIDAGRYVDLLEIDAASNTGIDNIREVLENAQYAPTAG 118
>gnl|CDD|180880 PRK07203, PRK07203, putative chlorohydrolase/aminohydrolase;
Validated.
Length = 442
Score = 28.0 bits (63), Expect = 3.3
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 12/48 (25%)
Query: 132 IYNNPSRTVIE-----------MDVDTMAELAATYPNIVGVKDATGKI 168
I +P++ VIE +++ T EL A YP+ DA GK+
Sbjct: 10 ITRDPAKPVIEDGAIAIEGNVIVEIGTTDELKAKYPDAE-FIDAKGKL 56
>gnl|CDD|152664 pfam12229, PG_binding_4, Putative peptidoglycan binding domain.
This domain is found associated with the
L,D-transpeptidase domain pfam03734. The structure of
this domain has been solved and shows a mixed alpha-beta
fold composed of nine beta strands and four alpha
helices. This domain is usually found to be duplicated.
Therefore, it seems likely that this domain acts to bind
the two unlinked peptidoglycan chains and bring them
into close association so they can be cross linked by
the transpeptidase domain (Bateman A pers. observation).
Length = 106
Score = 27.3 bits (61), Expect = 4.5
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 10 ITPFTKGNLIDEDAFVEHIEWQITEG 35
+TP G ID D ++ I I G
Sbjct: 76 VTPEVYGWKIDVDKLLKDIINAIKSG 101
>gnl|CDD|180022 PRK05333, PRK05333, NAD-dependent deacetylase; Provisional.
Length = 285
Score = 26.9 bits (60), Expect = 5.8
Identities = 13/26 (50%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 78 GSNNTRESVELAQYAHSIGADALLVV 103
G N RE V A+ A ADA+LVV
Sbjct: 197 GENVPRERVAAAR-AALDAADAVLVV 221
>gnl|CDD|183220 PRK11594, PRK11594, efflux system membrane protein; Provisional.
Length = 67
Score = 26.6 bits (59), Expect = 7.7
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 241 HQALFMEPAVCCVKYALSRLG 261
H ALF CC+ Y +SRL
Sbjct: 46 HPALFNTALYCCLFYLISRLF 66
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.320 0.135 0.392
Gapped
Lambda K H
0.267 0.0684 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,745,342
Number of extensions: 302182
Number of successful extensions: 630
Number of sequences better than 10.0: 1
Number of HSP's gapped: 612
Number of HSP's successfully gapped: 22
Length of query: 292
Length of database: 5,994,473
Length adjustment: 93
Effective length of query: 199
Effective length of database: 3,984,929
Effective search space: 793000871
Effective search space used: 793000871
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 (21.8 bits)
S2: 57 (25.8 bits)