RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7866
(109 letters)
>gnl|CDD|235432 PRK05367, PRK05367, glycine dehydrogenase; Provisional.
Length = 954
Score = 223 bits (570), Expect = 1e-69
Identities = 69/102 (67%), Positives = 84/102 (82%)
Query: 8 LGEHELLEEIQSIANKNEIWRSYIGLGYHNCLVPTVIQRNLFENPGWVTQYTPYQPEIAQ 67
L E E L E+++IA+KN+++RSYIG GY+ P VI RN+ ENP W T YTPYQPEI+Q
Sbjct: 58 LSEAEALAELRAIASKNKVFRSYIGQGYYGTHTPPVILRNILENPAWYTAYTPYQPEISQ 117
Query: 68 GRLESLLNFQTMVSDLTGLSVANASLLDEATAAAEAMSICHR 109
GRLE+LLNFQTMV+DLTGL +ANASLLDEATAAAEAM++ R
Sbjct: 118 GRLEALLNFQTMVADLTGLEIANASLLDEATAAAEAMALAKR 159
>gnl|CDD|216983 pfam02347, GDC-P, Glycine cleavage system P-protein. This family
consists of Glycine cleavage system P-proteins
EC:1.4.4.2 from bacterial, mammalian and plant sources.
The P protein is part of the glycine decarboxylase
multienzyme complex EC:2.1.2.10 (GDC) also annotated as
glycine cleavage system or glycine synthase. GDC
consists of four proteins P, H, L and T. The reaction
catalyzed by this protein is:- Glycine + lipoylprotein
<=> S-aminomethyldihydrolipoylprotein + CO2.
Length = 429
Score = 195 bits (497), Expect = 2e-62
Identities = 68/100 (68%), Positives = 88/100 (88%)
Query: 10 EHELLEEIQSIANKNEIWRSYIGLGYHNCLVPTVIQRNLFENPGWVTQYTPYQPEIAQGR 69
E+E+L E+++IA+KN+I++S+IG+GY++ ++P VI RN+ ENP W TQYTPYQPEI+QGR
Sbjct: 49 EYEMLAELEAIASKNKIYKSFIGMGYYDTIIPAVILRNILENPEWYTQYTPYQPEISQGR 108
Query: 70 LESLLNFQTMVSDLTGLSVANASLLDEATAAAEAMSICHR 109
LE+LLNFQTMV DLTGL VANASLLDE TAAAEAM++ R
Sbjct: 109 LEALLNFQTMVCDLTGLDVANASLLDEGTAAAEAMALAAR 148
>gnl|CDD|223480 COG0403, GcvP, Glycine cleavage system protein P
(pyridoxal-binding), N-terminal domain [Amino acid
transport and metabolism].
Length = 450
Score = 190 bits (484), Expect = 3e-60
Identities = 64/102 (62%), Positives = 81/102 (79%)
Query: 8 LGEHELLEEIQSIANKNEIWRSYIGLGYHNCLVPTVIQRNLFENPGWVTQYTPYQPEIAQ 67
L E+E L E++ IA+KN+++ S+IG GY++ P VI RN+ ENP W T YTPYQPEI+Q
Sbjct: 57 LSEYEALAELKEIASKNKVFTSFIGAGYYDTYTPPVILRNILENPEWYTAYTPYQPEISQ 116
Query: 68 GRLESLLNFQTMVSDLTGLSVANASLLDEATAAAEAMSICHR 109
GRLE+L FQT+V+DLTGL VANAS+LDEATAAAEAM + R
Sbjct: 117 GRLEALFEFQTLVADLTGLDVANASMLDEATAAAEAMLMAKR 158
>gnl|CDD|178035 PLN02414, PLN02414, glycine dehydrogenase (decarboxylating).
Length = 993
Score = 186 bits (474), Expect = 3e-56
Identities = 69/107 (64%), Positives = 92/107 (85%)
Query: 1 MTNFDMYLGEHELLEEIQSIANKNEIWRSYIGLGYHNCLVPTVIQRNLFENPGWVTQYTP 60
++ +D L E ++LE ++S+A+KN++++SYIG+GY+N VP VI RN+ ENPGW TQYTP
Sbjct: 78 LSKYDEGLTESQMLEHMKSLASKNKVFKSYIGMGYYNTHVPPVILRNILENPGWYTQYTP 137
Query: 61 YQPEIAQGRLESLLNFQTMVSDLTGLSVANASLLDEATAAAEAMSIC 107
YQ EIAQGRLESLLN+QTM++DLTGL ++NASLLDE TAAAEAM++C
Sbjct: 138 YQAEIAQGRLESLLNYQTMITDLTGLPMSNASLLDEGTAAAEAMAMC 184
Score = 25.9 bits (57), Expect = 5.5
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 4 FDMYLGEHELLEEIQSIANKN-EIWRSYIGLG 34
F+ Y EHELL + + NK+ + S I LG
Sbjct: 500 FNQYHSEHELLRYLHRLQNKDLSLVHSMIPLG 531
>gnl|CDD|129553 TIGR00461, gcvP, glycine dehydrogenase (decarboxylating). This
apparently ubiquitous enzyme is found in bacterial,
mammalian and plant sources. The enzyme catalyzes the
reaction: GLYCINE + LIPOYLPROTEIN =
S-AMINOMETHYL-DIHYDROLIPOYLPROTEIN + CO2. It is part of
the glycine decarboxylase multienzyme complex (GDC)
consisting of four proteins P, H, L and T. Active site
in E.coli is located as the (K) residues at position 713
of the SEED alignment [Energy metabolism, Amino acids
and amines].
Length = 939
Score = 165 bits (420), Expect = 6e-49
Identities = 68/100 (68%), Positives = 83/100 (83%)
Query: 10 EHELLEEIQSIANKNEIWRSYIGLGYHNCLVPTVIQRNLFENPGWVTQYTPYQPEIAQGR 69
E+E L ++ IA+KN ++SYIG+GY+ ++P VIQRNL ENPGW T YTPYQPEI+QGR
Sbjct: 48 EYEALAHLKKIASKNHKFKSYIGMGYYGTILPPVIQRNLLENPGWYTAYTPYQPEISQGR 107
Query: 70 LESLLNFQTMVSDLTGLSVANASLLDEATAAAEAMSICHR 109
LE+LLNFQT+VSDLTGL VANASLLDE TAAAEAM++
Sbjct: 108 LEALLNFQTVVSDLTGLPVANASLLDEGTAAAEAMALSFN 147
>gnl|CDD|171585 PRK12566, PRK12566, glycine dehydrogenase; Provisional.
Length = 954
Score = 154 bits (390), Expect = 6e-45
Identities = 66/102 (64%), Positives = 78/102 (76%)
Query: 8 LGEHELLEEIQSIANKNEIWRSYIGLGYHNCLVPTVIQRNLFENPGWVTQYTPYQPEIAQ 67
L E L ++ A +N++W S IG+GYH + PTVI RN+ ENPGW T YTPYQPEIAQ
Sbjct: 61 LDEQAALARLRGYAEQNQVWTSLIGMGYHGTVTPTVILRNVLENPGWYTAYTPYQPEIAQ 120
Query: 68 GRLESLLNFQTMVSDLTGLSVANASLLDEATAAAEAMSICHR 109
GRLE+LLNFQ M DLTGL +ANASLLDEATAAAEAM++ R
Sbjct: 121 GRLEALLNFQQMTIDLTGLDLANASLLDEATAAAEAMALAKR 162
>gnl|CDD|99737 cd00613, GDC-P, Glycine cleavage system P-protein, alpha- and
beta-subunits. This family consists of Glycine cleavage
system P-proteins EC:1.4.4.2 from bacterial, mammalian
and plant sources. The P protein is part of the glycine
decarboxylase multienzyme complex EC:2.1.2.10 (GDC) also
annotated as glycine cleavage system or glycine
synthase. GDC consists of four proteins P, H, L and T.
The reaction catalysed by this protein is: Glycine +
lipoylprotein <=> S-aminomethyldihydrolipoylprotein +
CO2. Alpha-beta-type dimers associate to form an
alpha(2)beta(2) tetramer, where the alpha- and
beta-subunits are structurally similar and appear to
have arisen by gene duplication and subsequent
divergence with a loss of one active site. The members
of this CD are widely dispersed among all three forms of
cellular life.
Length = 398
Score = 144 bits (365), Expect = 4e-43
Identities = 51/103 (49%), Positives = 70/103 (67%), Gaps = 4/103 (3%)
Query: 10 EHELLEEIQSIANKNEIWR---SYIGLGYHNCLVPTVIQRNLFENPGWVTQYTPYQPEIA 66
E E+L ++ +A+KN+ S++G G + P VI+RN+ EN + T YTPYQPEI+
Sbjct: 1 ETEVLRHLKRLASKNKALDQSMSFLGSGTYKHNPPAVIKRNILEN-EFYTAYTPYQPEIS 59
Query: 67 QGRLESLLNFQTMVSDLTGLSVANASLLDEATAAAEAMSICHR 109
QGRL++L QTM+ +LTG+ VANASL DEATAAAEA +
Sbjct: 60 QGRLQALFELQTMLCELTGMDVANASLQDEATAAAEAAGLAAI 102
>gnl|CDD|234769 PRK00451, PRK00451, glycine dehydrogenase subunit 1; Validated.
Length = 447
Score = 106 bits (267), Expect = 1e-28
Identities = 48/109 (44%), Positives = 68/109 (62%), Gaps = 12/109 (11%)
Query: 8 LGEHELLEEIQSIANKN---EIWRSYIGLGYHNCLVPTV----IQRNLFENPGWVTQYTP 60
L E ELL ++ +A KN E + S++G G ++ +P V I R+ F T YTP
Sbjct: 47 LSEMELLRHLRELAAKNKTAEEYPSFLGAGAYDHYIPAVVDHIISRSEF-----YTAYTP 101
Query: 61 YQPEIAQGRLESLLNFQTMVSDLTGLSVANASLLDEATAAAEAMSICHR 109
YQPEI+QG L+++ +QTM+ +LTG+ VANAS+ D ATA AEA + R
Sbjct: 102 YQPEISQGTLQAIFEYQTMICELTGMDVANASMYDGATALAEAALMAVR 150
>gnl|CDD|173865 cd08500, PBP2_NikA_DppA_OppA_like_4, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 499
Score = 31.8 bits (73), Expect = 0.041
Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 10/60 (16%)
Query: 19 SIA-NKNEIWRS-YIGLGYHNCLVP---TVIQRNLFENPGWVTQYTPYQPEIAQGRLESL 73
S+A N+ EI + Y GLG P V + + P W +Y Y P+ A L+
Sbjct: 271 SLAINREEIIETVYFGLG-----EPQQGPVSPGSPYYYPEWELKYYEYDPDKANKLLDEA 325
>gnl|CDD|238546 cd01126, TraG_VirD4, The TraG/TraD/VirD4 family are bacterial
conjugation proteins involved in type IV secretion.
These proteins aid the transfer of DNA from the plasmid
into the host bacterial chromosome. They contain an ATP
binding domain. VirD4 is involved in DNA transfer to
plant cells and is required for virulence.
Length = 384
Score = 27.4 bits (61), Expect = 1.8
Identities = 23/115 (20%), Positives = 31/115 (26%), Gaps = 17/115 (14%)
Query: 2 TNFDMYLGEH-ELLEEIQSIANKNEIWRSYIGLG-----YHNCLVPTVIQRN---LFENP 52
N G S+A+KN S L + N LV + L +
Sbjct: 160 RNDTNSSGPSPVAFSGYYSVASKNTKSGSIYALLSKLNLFANPLVAAATSSSDFDLRDLR 219
Query: 53 GWVTQY----TPYQPEIAQGRLESLLN--FQTMVSDLTGLSVANASL--LDEATA 99
T TP + + L N + L G L LDE
Sbjct: 220 KDKTLVFVGLTPDDLSRVRPIIGLLFNQIIDRLGRSLPGPEEKYRVLFLLDEFPL 274
>gnl|CDD|235292 PRK04366, PRK04366, glycine dehydrogenase subunit 2; Validated.
Length = 481
Score = 27.0 bits (61), Expect = 1.9
Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 60 PYQPE-IAQGRLESLLNFQTMVSDLTGL 86
P QPE QG LE + Q + ++TG+
Sbjct: 101 PLQPEETVQGALELMYELQEWLKEITGM 128
>gnl|CDD|185001 PRK15041, PRK15041, methyl-accepting chemotaxis protein I;
Provisional.
Length = 554
Score = 26.8 bits (59), Expect = 2.4
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 13/58 (22%)
Query: 55 VTQYTPYQPEIAQGRLESLLNFQTMVSDLTGLSVA--------NASLLDEATAAAEAM 104
VT+ T EIA E Q+ D GL+VA NA+L++E+ AAA A+
Sbjct: 449 VTRVTDIMGEIASASDE-----QSRGIDQVGLAVAEMDRVTQQNAALVEESAAAAAAL 501
>gnl|CDD|218168 pfam04602, Arabinose_trans, Mycobacterial cell wall arabinan
synthesis protein. Arabinosyltransferase is involved in
arabinogalactan (AG) biosynthesis pathway in
mycobacteria. AG is a component of the macromolecular
assembly of the mycolyl-AG-peptidoglycan complex of the
cell wall. This enzyme has important clinical
applications as it is believed to be the target of the
antimycobacterial drug Ethambutol.
Length = 1075
Score = 26.7 bits (59), Expect = 3.3
Identities = 14/62 (22%), Positives = 26/62 (41%), Gaps = 9/62 (14%)
Query: 18 QSIANKNEIWRSYIG---LGYHNCL-----VPTVIQRNLFENPGWVTQYTPYQPEIAQGR 69
Q A+ N W+ LG L + T ++ + + + G + +Y P P+ A
Sbjct: 997 QKEASSN-TWQDGANGGPLGITQLLLRASTISTYLRDDWYRDWGSLERYDPLVPDAAPAA 1055
Query: 70 LE 71
L+
Sbjct: 1056 LD 1057
>gnl|CDD|177843 PLN02191, PLN02191, L-ascorbate oxidase.
Length = 574
Score = 25.7 bits (56), Expect = 5.7
Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 59 TPYQPEIAQGRLESLLNFQTMVSDLTGLSVANASLLDEAT 98
+P P+ + RL LLN Q ++ T ++ N SL+ AT
Sbjct: 358 SPSPPKKYRKRL-ILLNTQNLIDGYTKWAINNVSLVTPAT 396
>gnl|CDD|236134 PRK07940, PRK07940, DNA polymerase III subunit delta'; Validated.
Length = 394
Score = 25.6 bits (57), Expect = 5.9
Identities = 10/40 (25%), Positives = 20/40 (50%)
Query: 66 AQGRLESLLNFQTMVSDLTGLSVANASLLDEATAAAEAMS 105
A+ R +LN ++ ++ A L+ A A A+A++
Sbjct: 219 ARARRAEVLNLALRLARVSDAVAAAEELVKAAEAEAKALT 258
>gnl|CDD|143806 pfam00015, MCPsignal, Methyl-accepting chemotaxis protein (MCP)
signalling domain. This domain is thought to transduce
the signal to CheA since it is highly conserved in very
diverse MCPs.
Length = 213
Score = 25.5 bits (56), Expect = 6.5
Identities = 9/28 (32%), Positives = 18/28 (64%)
Query: 78 TMVSDLTGLSVANASLLDEATAAAEAMS 105
V+ + ++ NA+L++E+ AAAE +
Sbjct: 170 QAVARIDQVTQQNAALVEESAAAAETLE 197
>gnl|CDD|236019 PRK07445, PRK07445, O-succinylbenzoic acid--CoA ligase; Reviewed.
Length = 452
Score = 25.3 bits (56), Expect = 8.2
Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 9/48 (18%)
Query: 11 HELLEEIQSIANKNEIWRSYIGLGYHNCLVPTVIQRNLFENPGWVTQY 58
L + N ++ + S LVPT +QR L P W+ Q+
Sbjct: 194 KRLKSGQELPPNPSDFFLS---------LVPTQLQRLLQLRPQWLAQF 232
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.132 0.395
Gapped
Lambda K H
0.267 0.0621 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,428,216
Number of extensions: 442027
Number of successful extensions: 447
Number of sequences better than 10.0: 1
Number of HSP's gapped: 444
Number of HSP's successfully gapped: 27
Length of query: 109
Length of database: 10,937,602
Length adjustment: 74
Effective length of query: 35
Effective length of database: 7,655,406
Effective search space: 267939210
Effective search space used: 267939210
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.4 bits)