Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate AO353_03500 AO353_03500 glycine dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_03500
(950 letters)
>FitnessBrowser__pseudo3_N2E3:AO353_03500
Length = 950
Score = 1896 bits (4911), Expect = 0.0
Identities = 950/950 (100%), Positives = 950/950 (100%)
Query: 1 MTQVNLSTANEFIARHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGL 60
MTQVNLSTANEFIARHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGL
Sbjct: 1 MTQVNLSTANEFIARHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGL 60
Query: 61 SEAEALASIKAIAAKNQLFKTYIGQGYYNCHTPSPILRNLLENPAWYTAYTPYQPEISQG 120
SEAEALASIKAIAAKNQLFKTYIGQGYYNCHTPSPILRNLLENPAWYTAYTPYQPEISQG
Sbjct: 61 SEAEALASIKAIAAKNQLFKTYIGQGYYNCHTPSPILRNLLENPAWYTAYTPYQPEISQG 120
Query: 121 RLEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASIHSHPQ 180
RLEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASIHSHPQ
Sbjct: 121 RLEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASIHSHPQ 180
Query: 181 TLDVLRTRAEPLGIDVVVGDERELTDVSAFFGALLQYPASNGDLFDYRELTERFHAVNAL 240
TLDVLRTRAEPLGIDVVVGDERELTDVSAFFGALLQYPASNGDLFDYRELTERFHAVNAL
Sbjct: 181 TLDVLRTRAEPLGIDVVVGDERELTDVSAFFGALLQYPASNGDLFDYRELTERFHAVNAL 240
Query: 241 VAVAADLLALTVLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLV 300
VAVAADLLALTVLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLV
Sbjct: 241 VAVAADLLALTVLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLV 300
Query: 301 GVSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLKQIAN 360
GVSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLKQIAN
Sbjct: 301 GVSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLKQIAN 360
Query: 361 RIHHLTAILAKGLSALGLNVEQANFFDTLTLATGANTAALHDKARAQRINLRVIDGERLG 420
RIHHLTAILAKGLSALGLNVEQANFFDTLTLATGANTAALHDKARAQRINLRVIDGERLG
Sbjct: 361 RIHHLTAILAKGLSALGLNVEQANFFDTLTLATGANTAALHDKARAQRINLRVIDGERLG 420
Query: 421 LSLDETTTQADIETLWSVLADGKALPDFAALAASVQSRIPAELVRQSPILSHPVFNRYHS 480
LSLDETTTQADIETLWSVLADGKALPDFAALAASVQSRIPAELVRQSPILSHPVFNRYHS
Sbjct: 421 LSLDETTTQADIETLWSVLADGKALPDFAALAASVQSRIPAELVRQSPILSHPVFNRYHS 480
Query: 481 ETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPPAQSAG 540
ETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPPAQSAG
Sbjct: 481 ETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPPAQSAG 540
Query: 541 YQQLTDELEAMLCAATGYDAISLQPNAGSQGEYAGLLAIRAYHQSRGEERRDICLIPSSA 600
YQQLTDELEAMLCAATGYDAISLQPNAGSQGEYAGLLAIRAYHQSRGEERRDICLIPSSA
Sbjct: 541 YQQLTDELEAMLCAATGYDAISLQPNAGSQGEYAGLLAIRAYHQSRGEERRDICLIPSSA 600
Query: 601 HGTNPATANMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGI 660
HGTNPATANMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGI
Sbjct: 601 HGTNPATANMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGI 660
Query: 661 REICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPI 720
REICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPI
Sbjct: 661 REICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPI 720
Query: 721 GVKSHLTPFLPGHAAMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAILNA 780
GVKSHLTPFLPGHAAMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAILNA
Sbjct: 721 GVKSHLTPFLPGHAAMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAILNA 780
Query: 781 NYISRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSF 840
NYISRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSF
Sbjct: 781 NYISRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSF 840
Query: 841 PVAGTLMIEPTESESKEELDRFCDAMICIREEIRAVENGTLDKDDNPLKNAPHTAAEIVG 900
PVAGTLMIEPTESESKEELDRFCDAMICIREEIRAVENGTLDKDDNPLKNAPHTAAEIVG
Sbjct: 841 PVAGTLMIEPTESESKEELDRFCDAMICIREEIRAVENGTLDKDDNPLKNAPHTAAEIVG 900
Query: 901 EWTHPYSREQAVYPVASLIEGKYWPPVGRVDNVFGDRNLICACPSIESYA 950
EWTHPYSREQAVYPVASLIEGKYWPPVGRVDNVFGDRNLICACPSIESYA
Sbjct: 901 EWTHPYSREQAVYPVASLIEGKYWPPVGRVDNVFGDRNLICACPSIESYA 950
Lambda K H
0.319 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: 2591
Number of extensions: 92
Number of successful extensions: 3
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: 950
Length of database: 950
Length adjustment: 44
Effective length of query: 906
Effective length of database: 906
Effective search space: 820836
Effective search space used: 820836
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 AO353_03500 AO353_03500 (glycine dehydrogenase)
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.7567.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 1499.5 0.0 0 1499.3 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 AO353_03500 glycine dehydrogenas
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 AO353_03500 glycine dehydrogenase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1499.3 0.0 0 0 1 939 [] 15 943 .. 15 943 .. 0.99
Alignments for each domain:
== domain 1 score: 1499.3 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkv 65
rh+Gp + + + ml++lGfd+l+al ++p++i+ + l le +e eala +k+ia+kn+ +
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 15 RHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGLSEAEALASIKAIAAKNQLF 79
9**************************************************************** PP
TIGR00461 66 ksyiGkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanas 130
k+yiG+Gyy+ +p i+rnllenp wytaytpyqpeisqGrleallnfqt+++dltGl++anas
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 80 KTYIGQGYYNCHTPSPILRNLLENPAWYTAYTPYQPEISQGRLEALLNFQTLISDLTGLPIANAS 144
***************************************************************** PP
TIGR00461 131 lldegtaaaeamalsfrvskkk.ankfvvakdvhpqtlevvktraeplgievivddaskvkkavd 194
llde+taaaeam +++r+sk+k + +f+ + + hpqtl+v++traeplgi+v+v+d +++++
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 145 LLDEATAAAEAMTFCKRLSKNKgSHAFFASIHSHPQTLDVLRTRAEPLGIDVVVGDERELTDVSA 209
**********************8899*************************************** PP
TIGR00461 195 vlGvllqypatdGeildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqrfGvp 259
+G+llqypa++G+++dy++l+++ + +alv+vaadllalt+ltppg++Gad+++GsaqrfGvp
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 210 FFGALLQYPASNGDLFDYRELTERFHAVNALVAVAADLLALTVLTPPGEFGADVAIGSAQRFGVP 274
***************************************************************** PP
TIGR00461 260 lGyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqhirrdkatsnictaqvll 324
lG+GGphaa+f++kd +kr +pGr+vGvs d+ G++alrla+qtreqhirr+katsnictaqvll
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 275 LGFGGPHAAYFSTKDAFKRDMPGRLVGVSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLL 339
***************************************************************** PP
TIGR00461 325 anvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaasevlka 389
an+as+yavyhGpkGlk+ia+ri++lt+ila+gl +++++++++fdtlt+ g ++a ++ +
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 340 ANIASMYAVYHGPKGLKQIANRIHHLTAILAKGLSALGLNVEQANFFDTLTLATGANTA-ALHDK 403
******************************************************99988.89999 PP
TIGR00461 390 aeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsedvansfpaellrdd 454
a+++ inlr ++ + +g++ldettt++d++ l+ vla + l+ + l v++ +pael r++
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 404 ARAQRINLRVIDGERLGLSLDETTTQADIETLWSVLADGKALP-DFAALAASVQSRIPAELVRQS 467
9***********************************9866554.8899***************** PP
TIGR00461 455 eilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpf 519
il ++vfnryhsetel+ryl +l kdlal+++miplGsctmklna+ em+p+tw ef+ +hpf
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 468 PILSHPVFNRYHSETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPF 532
***************************************************************** PP
TIGR00461 520 apaeqveGykeliaqlekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclip 584
ap+ q+ Gy++l +le+ l+ tG+daislqpn+G+qGeyaGl +ir yh+srgee+r+iclip
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 533 APPAQSAGYQQLTDELEAMLCAATGYDAISLQPNAGSQGEYAGLLAIRAYHQSRGEERRDICLIP 597
***************************************************************** PP
TIGR00461 585 asahGtnpasaamaGlkvvpvkcdkeGnidlvdlkakaekagdelaavmvtypstyGvfeetire 649
sahGtnpa+a+maG++vv+ +cd Gn+d++dl+aka ++ ++laa+m+typst+Gvfee+ire
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 598 SSAHGTNPATANMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGIRE 662
***************************************************************** PP
TIGR00461 650 vidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlhktfsiphGGGGpgmgpigvkshla 714
++ i+h GGqvy+dGanmna vGl++pg++G dv+hlnlhktf+iphGGGGpg+gpigvkshl+
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 663 ICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKSHLT 727
***************************************************************** PP
TIGR00461 715 pflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlkkasevailnanyla 779
pflp+ +++++ gav aap+Gsasilpi++myi+mmG Glk+as++ailnany+
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 728 PFLPG--------HAAMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAILNANYIS 784
*****........4688999********************************************* PP
TIGR00461 780 krlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptlsfpvaGtlmve 844
+rl+++y++l++g+++ vahecildlr+lk+ +gi++ dvakrl+d+Gfhapt+sfpvaGtlm+e
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 785 RRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSFPVAGTLMIE 849
***************************************************************** PP
TIGR00461 845 ptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaewadpysreeaay 909
pteses+eeldrf+dami+i+eei av +G+++++dn+lknaph+ +iv+ew++pysre+a+y
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 850 PTESESKEELDRFCDAMICIREEIRAVENGTLDKDDNPLKNAPHT-AAEIVGEWTHPYSREQAVY 913
********************************************5.6789*************** PP
TIGR00461 910 papvlkyfkfwptvarlddtyGdrnlvcsc 939
p++ l + k+wp v+r+d+++Gdrnl+c+c
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 914 PVASLIEGKYWPPVGRVDNVFGDRNLICAC 943
*****************************9 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (950 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: 0.05u 0.03s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 11.22
//
[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