Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate 6938616 Sama_2719 glycine dehydrogenase (RefSeq)
Query= reanno::Koxy:BWI76_RS23870
(957 letters)
>FitnessBrowser__SB2B:6938616
Length = 962
Score = 1355 bits (3506), Expect = 0.0
Identities = 662/960 (68%), Positives = 791/960 (82%), Gaps = 6/960 (0%)
Query: 3 QTLGQLENRDAFIERHIGPDALQQQEMLKTVGADSLNALIGQIVPQDIQLATPPQVGEAT 62
QTL +LE + F+ RHIGPDA +QQ ML VGA+SL L QIVP+ I+L VG +
Sbjct: 4 QTLTELEQHELFLTRHIGPDADEQQAMLNYVGAESLEDLTAQIVPESIRLGRELNVGASN 63
Query: 63 TEFAALAELKAIAGRNKRFKSYIGMGYTAVQLPPVIQRNMLENPGWYTAYTPYQPEVSQG 122
E A LA ++ +A +N+ FKSYIGMGY ++P VI RN+LENPGWYTAYTPYQPE++QG
Sbjct: 64 GEAAGLAYIRQLADKNQVFKSYIGMGYHGTEVPNVILRNVLENPGWYTAYTPYQPEIAQG 123
Query: 123 RLESLLNFQQVTLDLTGLDIASASLLDEATAAAEAMAMAKRVSKLKNANRFFVAADVHPQ 182
RLE++LNFQQ+++DLTGLD+ASASLLDEATAAAEAMA+AKRVSK K AN FFVA DV PQ
Sbjct: 124 RLEAILNFQQLSIDLTGLDLASASLLDEATAAAEAMALAKRVSKAKKANTFFVADDVFPQ 183
Query: 183 TLDVVRTRAETFGFDVIVDDAEKALDHQDVFGVLLQQVGTTGEVHDYSKLIADLKARKVI 242
TLDVV+TRAE FGFD++ A +A +H D+FG L Q G++ D+++L A L+A+ VI
Sbjct: 184 TLDVVKTRAECFGFDIVTGPAAEAANHDDLFGALFQYTNRQGQLTDFTELFAQLRAKNVI 243
Query: 243 VSVAADFMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEFKRSMPGRII 302
V+V AD M+LVLL +PG GAD+VFGSAQRFGVPMG+GGPHAAFF +KDE KRSMPGRII
Sbjct: 244 VTVGADIMSLVLLKSPGAMGADVVFGSAQRFGVPMGFGGPHAAFFVSKDEHKRSMPGRII 303
Query: 303 GVSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVFHGPAGLKRIAS 362
GVSKD G TALRMAMQTREQHIRREKANSNICT+QVLLAN+AS YAVFHGP GLK IA+
Sbjct: 304 GVSKDTRGKTALRMAMQTREQHIRREKANSNICTAQVLLANMASFYAVFHGPQGLKVIAN 363
Query: 363 RIHRLTDILADGLQKKGLKLRHAHYFDTLCVEVADKAAVLARAEALRINLRSDIHHAVGI 422
RIHRLTDILA GL KG+ + + +FDTL +V D AV ARA A +NLR D VG+
Sbjct: 364 RIHRLTDILAAGLAAKGVTVLNTQWFDTLSFKV-DVDAVRARALAAGVNLRYDADGVVGV 422
Query: 423 TLDEATTREDVLNLFRAILGDDHGLDIDTLDKDV-ALDSRSIPASMLRDDAILTHPVFNR 481
+L E TTR DV LF ILG HGLD+ +D D+ A S SIPA+++R++A LTHP FN
Sbjct: 423 SLAETTTRADVAELFDIILGAGHGLDVAAIDADILAKGSSSIPAALVREEAFLTHPTFNS 482
Query: 482 YHSETEMMRYMHALERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPVDQ 541
YHSETEMMRY+ LE KDLALN +MI LGSCTMKLNAA EMIP++WPEFA +HPFCP +Q
Sbjct: 483 YHSETEMMRYIKRLENKDLALNHSMISLGSCTMKLNAAVEMIPVSWPEFANMHPFCPSEQ 542
Query: 542 AEGYHQMIAQLSDWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLIP 601
A+GY Q+I +LSDWLV +TGYDAVCMQPNSGAQGEYAGLLAIR YHESR EGHRD+CLIP
Sbjct: 543 AQGYTQLIGELSDWLVDITGYDAVCMQPNSGAQGEYAGLLAIRKYHESRGEGHRDVCLIP 602
Query: 602 SSAHGTNPASAQMAGMQVVVVACDKNGNIDLADLRAKAEQHAANLSCIMVTYPSTHGVYE 661
SAHGTNPASAQ+AGM+VVV ACDK GN+DL DLRAKA + A NLSCIM+TYPSTHGVYE
Sbjct: 603 QSAHGTNPASAQLAGMKVVVTACDKQGNVDLDDLRAKAAEVAENLSCIMITYPSTHGVYE 662
Query: 662 ETIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPGM 721
ET+RE+C+++HQ GGQVYLDGANMNAQVG+T+PGFIGADVSHLNLHKTF IPHGGGGPGM
Sbjct: 663 ETVREICDIIHQHGGQVYLDGANMNAQVGLTAPGFIGADVSHLNLHKTFAIPHGGGGPGM 722
Query: 722 GPIGVKSHLAQFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKQA 781
GPIGVK HLA FV GH+VV+ GAVSAAPFGSA ILPISWMYI+++G++GLKQ+
Sbjct: 723 GPIGVKKHLAPFVAGHAVVKQGIESDNNGAVSAAPFGSAGILPISWMYIKLLGSKGLKQS 782
Query: 782 SQMAILNANYIATRLKDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDFG 841
+Q A+LNANY+ +L + +PVLY GR+ R+AHECI+D+RPLKE +G++E+D+AKRL D+G
Sbjct: 783 TQTAMLNANYLTKKLSEHYPVLYRGRNDRIAHECIIDMRPLKEASGVTEMDVAKRLNDYG 842
Query: 842 FHAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRGEIDRVKAGEWPLEDNPLVNAP 901
FHAPTMSFPVAGTLM+EPTESESK ELDRFI+AM+AIRGEI RV++GEWP+++NPL NAP
Sbjct: 843 FHAPTMSFPVAGTLMIEPTESESKAELDRFIEAMVAIRGEIARVESGEWPVDNNPLANAP 902
Query: 902 HTQGELVSAW--NHPYARELAVFP--AGLNNKYWPTVKRLDDVYGDRNLFCSCVPMSEYQ 957
HT +++ + PY+RELAVFP + NK+WPTV R+DDVYGDRNLFC+CVPMS+Y+
Sbjct: 903 HTMDDIMDPAFDSRPYSRELAVFPTESVRANKFWPTVNRIDDVYGDRNLFCACVPMSDYE 962
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: 2281
Number of extensions: 82
Number of successful extensions: 7
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: 962
Length adjustment: 44
Effective length of query: 913
Effective length of database: 918
Effective search space: 838134
Effective search space used: 838134
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 6938616 Sama_2719 (glycine dehydrogenase (RefSeq))
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.1912.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 1530.5 0.1 0 1530.3 0.1 1.0 1 lcl|FitnessBrowser__SB2B:6938616 Sama_2719 glycine dehydrogenase
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6938616 Sama_2719 glycine dehydrogenase (RefSeq)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1530.3 0.1 0 0 1 939 [] 18 955 .. 18 955 .. 0.98
Alignments for each domain:
== domain 1 score: 1530.3 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyiGkGyyati 77
rh+Gpd+ eq+ ml+ +G+++l++l+ q+vp++irl r l+++a++ e + la ++++a+kn+++ksyiG+Gy +t
lcl|FitnessBrowser__SB2B:6938616 18 RHIGPDADEQQAMLNYVGAESLEDLTAQIVPESIRLGRELNVGASNGEAAGLAYIRQLADKNQVFKSYIGMGYHGTE 94
9**************************************************************************** PP
TIGR00461 78 lppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaaaeamalsfrvskkk.a 153
+p vi+rn+lenpgwytaytpyqpei+qGrlea+lnfq++ +dltGl++a+asllde+taaaeamal++rvsk k a
lcl|FitnessBrowser__SB2B:6938616 95 VPNVILRNVLENPGWYTAYTPYQPEIAQGRLEAILNFQQLSIDLTGLDLASASLLDEATAAAEAMALAKRVSKAKkA 171
*************************************************************************8879 PP
TIGR00461 154 nkfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdGeildykalidelksrkalvsvaa 230
n f+va+dv pqtl+vvktrae +g++++ + a + ++ d++G+l qy+ +G++ d+++l +l+ ++++v+v a
lcl|FitnessBrowser__SB2B:6938616 172 NTFFVADDVFPQTLDVVKTRAECFGFDIVTGPAAEAANHDDLFGALFQYTNRQGQLTDFTELFAQLRAKNVIVTVGA 248
***************************************************************************** PP
TIGR00461 231 dllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqh 307
d+++l+ll++pg +Gad+v+GsaqrfGvp+G+GGphaaff +kde+kr++pGri+Gvskd+ G+talr+a+qtreqh
lcl|FitnessBrowser__SB2B:6938616 249 DIMSLVLLKSPGAMGADVVFGSAQRFGVPMGFGGPHAAFFVSKDEHKRSMPGRIIGVSKDTRGKTALRMAMQTREQH 325
***************************************************************************** PP
TIGR00461 308 irrdkatsnictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaas 384
irr+ka+snictaqvllan+as yav+hGp+Glk ia+ri+rlt+ilaagl k+ + n ++fdtl+ +v +a
lcl|FitnessBrowser__SB2B:6938616 326 IRREKANSNICTAQVLLANMASFYAVFHGPQGLKVIANRIHRLTDILAAGLAAKGVTVLNTQWFDTLSFKVDVDA-- 400
**********************************************************************97554.. PP
TIGR00461 385 evlkaaeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsedvan....sfpaellrddeil 457
v +a +a++nlr + + vg++l ettt++dv +l+++++g +gl++ ++ d+ s+pa+l r++ +l
lcl|FitnessBrowser__SB2B:6938616 401 -VRARALAAGVNLRYDADGVVGVSLAETTTRADVAELFDIILG-AGHGLDVAAIDADILAkgssSIPAALVREEAFL 475
.699999************************************.55*****9999998655666************* PP
TIGR00461 458 rdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykeliaq 534
+++ fn yhsete++ry++rle+kdlaln+smi lGsctmklna++em+p++wpefa++hpf+p+eq++Gy +li +
lcl|FitnessBrowser__SB2B:6938616 476 THPTFNSYHSETEMMRYIKRLENKDLALNHSMISLGSCTMKLNAAVEMIPVSWPEFANMHPFCPSEQAQGYTQLIGE 552
***************************************************************************** PP
TIGR00461 535 lekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeG 611
l +wlv+itG+da+++qpnsGaqGeyaGl +ir+yhesrge+hr++clip+sahGtnpasa++aG+kvv+ +cdk+G
lcl|FitnessBrowser__SB2B:6938616 553 LSDWLVDITGYDAVCMQPNSGAQGEYAGLLAIRKYHESRGEGHRDVCLIPQSAHGTNPASAQLAGMKVVVTACDKQG 629
***************************************************************************** PP
TIGR00461 612 nidlvdlkakaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchln 688
n+dl dl+aka + +++l+++m+typst+Gv+eet+re++di+h+ GGqvyldGanmnaqvGlt+pg++Gadv+hln
lcl|FitnessBrowser__SB2B:6938616 630 NVDLDDLRAKAAEVAENLSCIMITYPSTHGVYEETVREICDIIHQHGGQVYLDGANMNAQVGLTAPGFIGADVSHLN 706
***************************************************************************** PP
TIGR00461 689 lhktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlk 765
lhktf+iphGGGGpgmgpigvk hlapf+ + + vv+ es + gavsaap+Gsa ilpis+myik++G++Glk
lcl|FitnessBrowser__SB2B:6938616 707 LHKTFAIPHGGGGPGMGPIGVKKHLAPFVAG---HAVVKQGIESDNNGAVSAAPFGSAGILPISWMYIKLLGSKGLK 780
*******************************...777888889999******************************* PP
TIGR00461 766 kasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptlsfpvaGtlm 842
++++ a+lnanyl+k+l ++y++l++gr++r+aheci+d+r+lke +g+ ++dvakrl dyGfhapt+sfpvaGtlm
lcl|FitnessBrowser__SB2B:6938616 781 QSTQTAMLNANYLTKKLSEHYPVLYRGRNDRIAHECIIDMRPLKEASGVTEMDVAKRLNDYGFHAPTMSFPVAGTLM 857
***************************************************************************** PP
TIGR00461 843 veptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaew.adpysreeaaypapvlkyfk 918
+epteses+ eldrfi+am+ai+ ei v +Ge++ ++n+l naph++++ + + pysre a++p ++ +k
lcl|FitnessBrowser__SB2B:6938616 858 IEPTESESKAELDRFIEAMVAIRGEIARVESGEWPVDNNPLANAPHTMDDIMDPAFdSRPYSRELAVFPTESVRANK 934
*************************************************99987661567***************** PP
TIGR00461 919 fwptvarlddtyGdrnlvcsc 939
fwptv+r+dd+yGdrnl+c+c
lcl|FitnessBrowser__SB2B:6938616 935 FWPTVNRIDDVYGDRNLFCAC 955
********************9 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (962 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 13.40
//
[ok]
This GapMind analysis is from Sep 17 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