Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate WP_086511408.1 BZY95_RS18725 glycine dehydrogenase (aminomethyl-transferring)
Query= reanno::Koxy:BWI76_RS23870
(957 letters)
>NCBI__GCF_002151265.1:WP_086511408.1
Length = 964
Score = 1214 bits (3140), Expect = 0.0
Identities = 615/957 (64%), Positives = 731/957 (76%), Gaps = 5/957 (0%)
Query: 5 LGQLENRDAFIERHIGPDALQQQEMLKTVGADSLNALIGQIVPQDIQLATPPQVGEATTE 64
L +L + DAFI RH GP ML + +SL LI + VP DI+L + +E
Sbjct: 8 LAELADHDAFIRRHNGPGTEDVAAMLAALDMESLETLIERTVPADIRLGRELDLDPPRSE 67
Query: 65 FAALAELKAIAGRNKRFKSYIGMGYTAVQLPPVIQRNMLENPGWYTAYTPYQPEVSQGRL 124
AL LK +A +NK FK+YIG GY +P VIQRN+LENPGWYTAYTPYQPE++QGRL
Sbjct: 68 AEALDYLKRLARQNKVFKTYIGQGYYNTHVPAVIQRNVLENPGWYTAYTPYQPEIAQGRL 127
Query: 125 ESLLNFQQVTLDLTGLDIASASLLDEATAAAEAMAMAKRVSKLKNANRFFVAADVHPQTL 184
E LLNFQQ+ +DLTG+++A+ASLLDEATAAAEAMA+ +R +K +N FFVA DV PQTL
Sbjct: 128 EGLLNFQQMVMDLTGMELANASLLDEATAAAEAMALCQRANKKSKSNAFFVADDVLPQTL 187
Query: 185 DVVRTRAETFGFDVIVDDAEKALDHQDVFGVLLQQVGTTGEVHDYSKLIADLKARKVIVS 244
DVVRTRA FGF++IV AE +H DVFG LLQ G +G VHD + L+A + R V+
Sbjct: 188 DVVRTRAYYFGFELIVGPAESLAEH-DVFGALLQYPGESGRVHDLAPLLATARERNVMTC 246
Query: 245 VAADFMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEFKRSMPGRIIGV 304
VAAD M+LVLL PG GADIV G+ QRFGVPMGYGGPHAA+FA D KRS+PGRIIGV
Sbjct: 247 VAADIMSLVLLKEPGALGADIVVGNTQRFGVPMGYGGPHAAYFATTDSLKRSIPGRIIGV 306
Query: 305 SKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVFHGPAGLKRIASRI 364
S+DA GNTALRMAMQTREQHIRREKA SNICT+Q LLANIA YAV+HG GL IA+RI
Sbjct: 307 SRDARGNTALRMAMQTREQHIRREKATSNICTAQALLANIAGFYAVYHGAEGLTTIATRI 366
Query: 365 HRLTDILADGLQKKGLKLRHAHYFDTLCVEVADKAAVLARAEALRINLRSDIHHAVGITL 424
HRLT ILA GL++KG++L H +FDTL + D + RA INLR +G++L
Sbjct: 367 HRLTTILAVGLKEKGVRLAHDSWFDTLRLTGVDAGKIHGRALTHEINLRYFEGGDIGVSL 426
Query: 425 DEATTREDVLNLFRAILGDDHGLDIDTLDKDVALDSRS-IPASMLRDDAILTHPVFNRYH 483
DE TT D+ LF +LG++HGL I LD+ +A + S IPA+ R+ A LTHP F R+
Sbjct: 427 DETTTAHDLDVLFDVLLGEEHGLSITALDERIAAEGISGIPAASRRESAFLTHPNFKRFR 486
Query: 484 SETEMMRYMHALERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPVDQAE 543
SETEM+RY+ LE KDL+L AMIPLGSCTMKLNA +EMIPITWPEF +LHPF P +QA
Sbjct: 487 SETEMLRYLKRLENKDLSLTHAMIPLGSCTMKLNATSEMIPITWPEFGQLHPFVPQEQAV 546
Query: 544 GYHQMIAQLSDWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLIPSS 603
GY QMI +L+ +LV++TGYD + MQPNSGAQGEYAGL+AIR Y ++ EGHRD+CLIPSS
Sbjct: 547 GYKQMIDELAAFLVEITGYDHISMQPNSGAQGEYAGLVAIRRYQAAQGEGHRDVCLIPSS 606
Query: 604 AHGTNPASAQMAGMQVVVVACDKNGNIDLADLRAKAEQHAANLSCIMVTYPSTHGVYEET 663
AHGTNPASA MA M+VVVV CD NGNIDL DLRAKAE+H+ LS IM+TYPSTHGV+EE
Sbjct: 607 AHGTNPASAAMAQMKVVVVECDSNGNIDLDDLRAKAEKHSEALSAIMLTYPSTHGVFEEG 666
Query: 664 IREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPGMGP 723
IRE C +VH+ GGQVY+DGANMNAQVG++ PG G DVSHLNLHKTFCIPHGGGGPGMGP
Sbjct: 667 IREACAIVHRHGGQVYIDGANMNAQVGLSRPGDFGGDVSHLNLHKTFCIPHGGGGPGMGP 726
Query: 724 IGVKSHLAQFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKQASQ 783
IGVK+HLA +V H V I G+ GAVSAA FGSASILPISW YI+MMGA GL+QA++
Sbjct: 727 IGVKAHLAPYVSNHVVTPIAGVNENCGAVSAAAFGSASILPISWAYIKMMGARGLRQATE 786
Query: 784 MAILNANYIATRLKDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDFGFH 843
+AILNANYIA RL+ +PVLY G +G VAHECI+DIRPLK +GISE DIAKRL+D+GFH
Sbjct: 787 LAILNANYIARRLEAHYPVLYRGVNGTVAHECIIDIRPLKSASGISEEDIAKRLMDYGFH 846
Query: 844 APTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRGEIDRVKAGEWPLEDNPLVNAPHT 903
APTMSFPV GTLMVEPTESES+ E+DRF DAM+AIR EI RV+ GEWP +DNPLVNAPHT
Sbjct: 847 APTMSFPVPGTLMVEPTESESRYEIDRFCDAMIAIREEIARVERGEWPADDNPLVNAPHT 906
Query: 904 QGELVS-AWNHPYARELAVFP--AGLNNKYWPTVKRLDDVYGDRNLFCSCVPMSEYQ 957
+L+ AW Y+RE+A FP A KYWP V R+D+V+GDR L CSC + EY+
Sbjct: 907 MADLMDPAWERAYSREVAAFPSEAVKAAKYWPAVNRVDNVFGDRQLICSCPSIDEYR 963
Lambda K H
0.320 0.135 0.399
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 2234
Number of extensions: 94
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 957
Length of database: 964
Length adjustment: 44
Effective length of query: 913
Effective length of database: 920
Effective search space: 839960
Effective search space used: 839960
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 (26.6 bits)
Align candidate WP_086511408.1 BZY95_RS18725 (glycine dehydrogenase (aminomethyl-transferring))
to HMM TIGR00461 (gcvP: glycine dehydrogenase (EC 1.4.4.2))
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: ../tmp/path.carbon/TIGR00461.hmm
# target sequence database: /tmp/gapView.3147.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR00461 [M=939]
Accession: TIGR00461
Description: gcvP: glycine dehydrogenase
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
0 1506.1 0.0 0 1506.0 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086511408.1 BZY95_RS18725 glycine dehydrogen
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086511408.1 BZY95_RS18725 glycine dehydrogenase (aminomethyl-transferring)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1506.0 0.0 0 0 1 939 [] 20 956 .. 20 956 .. 0.98
Alignments for each domain:
== domain 1 score: 1506.0 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyi 69
rh Gp++ ++ ml +l +++l+ lie+ vp dirl r l l+ p +e eal lk++a +nk++k+yi
lcl|NCBI__GCF_002151265.1:WP_086511408.1 20 RHNGPGTEDVAAMLAALDMESLETLIERTVPADIRLGRELDLDPPRSEAEALDYLKRLARQNKVFKTYI 88
8******************************************************************** PP
TIGR00461 70 GkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaa 138
G+Gyy+t +p viqrn+lenpgwytaytpyqpei+qGrle llnfq++v+dltG+e+anasllde+taa
lcl|NCBI__GCF_002151265.1:WP_086511408.1 89 GQGYYNTHVPAVIQRNVLENPGWYTAYTPYQPEIAQGRLEGLLNFQQMVMDLTGMELANASLLDEATAA 157
********************************************************************* PP
TIGR00461 139 aeamalsfrvskk.kankfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatd 206
aeamal++r kk k+n+f+va+dv pqtl+vv+tra +g+e+iv+ a+++ + dv+G+llqyp+ +
lcl|NCBI__GCF_002151265.1:WP_086511408.1 158 AEAMALCQRANKKsKSNAFFVADDVLPQTLDVVRTRAYYFGFELIVGPAESLAE-HDVFGALLQYPGES 225
********99865279*********************************99876.59************ PP
TIGR00461 207 GeildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkde 275
G ++d+ l +++r+++ +vaad+++l+ll+ pg lGadiv+G +qrfGvp+GyGGphaa+fa+ d
lcl|NCBI__GCF_002151265.1:WP_086511408.1 226 GRVHDLAPLLATARERNVMTCVAADIMSLVLLKEPGALGADIVVGNTQRFGVPMGYGGPHAAYFATTDS 294
********************************************************************* PP
TIGR00461 276 ykrklpGrivGvskdalGntalrlalqtreqhirrdkatsnictaqvllanvaslyavyhGpkGlknia 344
+kr++pGri+Gvs+da Gntalr+a+qtreqhirr+katsnictaq+llan+a yavyhG+ Gl ia
lcl|NCBI__GCF_002151265.1:WP_086511408.1 295 LKRSIPGRIIGVSRDARGNTALRMAMQTREQHIRREKATSNICTAQALLANIAGFYAVYHGAEGLTTIA 363
********************************************************************* PP
TIGR00461 345 rrifrltsilaaglkrknyelrnktyfdtltvevgekaasevlkaaeeaeinlravvltevgialdett 413
+ri+rlt+ila+glk+k+ +l ++ +fdtl++ + ++ +a ++einlr +++g++ldett
lcl|NCBI__GCF_002151265.1:WP_086511408.1 364 TRIHRLTTILAVGLKEKGVRLAHDSWFDTLRLTGVDA--GKIHGRALTHEINLRYFEGGDIGVSLDETT 430
******************************9875554..36**************************** PP
TIGR00461 414 tkedvldllkvlagkdnlglsseelsedvan....sfpaellrddeilrdevfnryhsetellrylhrl 478
t +d+ l++vl+g++ +gls+ l+e +a +pa+ +r++ +l+++ f+r+ sete+lryl+rl
lcl|NCBI__GCF_002151265.1:WP_086511408.1 431 TAHDLDVLFDVLLGEE-HGLSITALDERIAAegisGIPAASRRESAFLTHPNFKRFRSETEMLRYLKRL 498
**************76.**********999878878********************************* PP
TIGR00461 479 eskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykeliaqlekwlveitGfda 547
e+kdl+l+++miplGsctmklnat em+pitwpef+++hpf p eq+ Gyk++i +l++ lveitG+d
lcl|NCBI__GCF_002151265.1:WP_086511408.1 499 ENKDLSLTHAMIPLGSCTMKLNATSEMIPITWPEFGQLHPFVPQEQAVGYKQMIDELAAFLVEITGYDH 567
********************************************************************* PP
TIGR00461 548 islqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeGnidlv 616
is+qpnsGaqGeyaGl +ir+y+ ++ge+hr++clip sahGtnpasaama +kvv+v+cd +Gnidl
lcl|NCBI__GCF_002151265.1:WP_086511408.1 568 ISMQPNSGAQGEYAGLVAIRRYQAAQGEGHRDVCLIPSSAHGTNPASAAMAQMKVVVVECDSNGNIDLD 636
********************************************************************* PP
TIGR00461 617 dlkakaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvc 685
dl+akaek+++ l+a+m+typst+Gvfee+ire++ ivhr GGqvy+dGanmnaqvGl++pgd+G dv+
lcl|NCBI__GCF_002151265.1:WP_086511408.1 637 DLRAKAEKHSEALSAIMLTYPSTHGVFEEGIREACAIVHRHGGQVYIDGANMNAQVGLSRPGDFGGDVS 705
********************************************************************* PP
TIGR00461 686 hlnlhktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisym 754
hlnlhktf+iphGGGGpgmgpigvk+hlap++ + + v + g +++ gavsaa +Gsasilpis++
lcl|NCBI__GCF_002151265.1:WP_086511408.1 706 HLNLHKTFCIPHGGGGPGMGPIGVKAHLAPYVSN---HVVTPIAGVNENCGAVSAAAFGSASILPISWA 771
*********************************9...55667789999********************* PP
TIGR00461 755 yikmmGaeGlkkasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrl 823
yikmmGa+Gl++a+e+ailnany+a+rl+ +y++l++g ++ vaheci+d+r+lk +gi+++d+akrl
lcl|NCBI__GCF_002151265.1:WP_086511408.1 772 YIKMMGARGLRQATELAILNANYIARRLEAHYPVLYRGVNGTVAHECIIDIRPLKSASGISEEDIAKRL 840
********************************************************************* PP
TIGR00461 824 ldyGfhaptlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqs 892
+dyGfhapt+sfpv+Gtlmvepteses+ e+drf+damiai+eei v Ge++++dn+l+naph++ +
lcl|NCBI__GCF_002151265.1:WP_086511408.1 841 MDYGFHAPTMSFPVPGTLMVEPTESESRYEIDRFCDAMIAIREEIARVERGEWPADDNPLVNAPHTMAD 909
********************************************************************* PP
TIGR00461 893 livaewadpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
l+ w +ysre+aa+p +k k+wp+v+r+d+++Gdr+l+csc
lcl|NCBI__GCF_002151265.1:WP_086511408.1 910 LMDPAWERAYSREVAAFPSEAVKAAKYWPAVNRVDNVFGDRQLICSC 956
*********************************************** PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (964 residues searched)
Passed MSV filter: 1 (1); expected 0.0 (0.02)
Passed bias filter: 1 (1); expected 0.0 (0.02)
Passed Vit filter: 1 (1); expected 0.0 (0.001)
Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
Initial search space (Z): 1 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.06
# Mc/sec: 13.32
//
[ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory