Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate Pf6N2E2_5558 Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2)
Query= reanno::pseudo6_N2E2:Pf6N2E2_5558
(953 letters)
>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5558
Length = 953
Score = 1899 bits (4918), Expect = 0.0
Identities = 953/953 (100%), Positives = 953/953 (100%)
Query: 1 MTVNLGTANEFIARHIGPRASDEQAMLERLGYDSLEALSASVIPESIKGTSVLDMGDGQS 60
MTVNLGTANEFIARHIGPRASDEQAMLERLGYDSLEALSASVIPESIKGTSVLDMGDGQS
Sbjct: 1 MTVNLGTANEFIARHIGPRASDEQAMLERLGYDSLEALSASVIPESIKGTSVLDMGDGQS 60
Query: 61 EADALASIKAIAAKNQLFKTYIGQGYYNCHTPAPILRNLLENPAWYTAYTPYQPEISQGR 120
EADALASIKAIAAKNQLFKTYIGQGYYNCHTPAPILRNLLENPAWYTAYTPYQPEISQGR
Sbjct: 61 EADALASIKAIAAKNQLFKTYIGQGYYNCHTPAPILRNLLENPAWYTAYTPYQPEISQGR 120
Query: 121 LEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSNAFFASVHSHPQT 180
LEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSNAFFASVHSHPQT
Sbjct: 121 LEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSNAFFASVHSHPQT 180
Query: 181 LDVLRTRAEPLGIDVVVGDERELSDVSGFFGALLQYPASNGDLFDYRELTERFHTANALV 240
LDVLRTRAEPLGIDVVVGDERELSDVSGFFGALLQYPASNGDLFDYRELTERFHTANALV
Sbjct: 181 LDVLRTRAEPLGIDVVVGDERELSDVSGFFGALLQYPASNGDLFDYRELTERFHTANALV 240
Query: 241 AVAADLLALTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVG 300
AVAADLLALTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVG
Sbjct: 241 AVAADLLALTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVG 300
Query: 301 VSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLVQIANR 360
VSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLVQIANR
Sbjct: 301 VSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLVQIANR 360
Query: 361 IHHLTAILAKGLGALGLSVEQESFFDTLTLRTGAQTAALHDKARAQRINLRVVDAERLGL 420
IHHLTAILAKGLGALGLSVEQESFFDTLTLRTGAQTAALHDKARAQRINLRVVDAERLGL
Sbjct: 361 IHHLTAILAKGLGALGLSVEQESFFDTLTLRTGAQTAALHDKARAQRINLRVVDAERLGL 420
Query: 421 SLDETTSQADVEALLRLIGNLMADGKAVPDFAALAASVQSHIPAELVRQSAILSHPVFNR 480
SLDETTSQADVEALLRLIGNLMADGKAVPDFAALAASVQSHIPAELVRQSAILSHPVFNR
Sbjct: 421 SLDETTSQADVEALLRLIGNLMADGKAVPDFAALAASVQSHIPAELVRQSAILSHPVFNR 480
Query: 481 YHSETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQ 540
YHSETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQ
Sbjct: 481 YHSETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQ 540
Query: 541 SAGYQQLTDELEAMLCAATGYDAVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIP 600
SAGYQQLTDELEAMLCAATGYDAVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIP
Sbjct: 541 SAGYQQLTDELEAMLCAATGYDAVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIP 600
Query: 601 SSAHGTNPATAHMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFE 660
SSAHGTNPATAHMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFE
Sbjct: 601 SSAHGTNPATAHMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFE 660
Query: 661 EGIREICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGV 720
EGIREICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGV
Sbjct: 661 EGIREICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGV 720
Query: 721 GPIGVKSHLAPFLPGHASMERKQGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAI 780
GPIGVKSHLAPFLPGHASMERKQGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAI
Sbjct: 721 GPIGVKSHLAPFLPGHASMERKQGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAI 780
Query: 781 LNANYIARRLEEHYPVLYSGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPT 840
LNANYIARRLEEHYPVLYSGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPT
Sbjct: 781 LNANYIARRLEEHYPVLYSGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPT 840
Query: 841 MSFPVAGTLMIEPTESESKEELDRFCDAMICIREEIRAVENGSLDKDDNPLKNAPHTAAE 900
MSFPVAGTLMIEPTESESKEELDRFCDAMICIREEIRAVENGSLDKDDNPLKNAPHTAAE
Sbjct: 841 MSFPVAGTLMIEPTESESKEELDRFCDAMICIREEIRAVENGSLDKDDNPLKNAPHTAAE 900
Query: 901 IVGEWTHPYSREQAVYPVASLIDGKYWPPVGRVDNVFGDRNLVCACPSIESYA 953
IVGEWTHPYSREQAVYPVASLIDGKYWPPVGRVDNVFGDRNLVCACPSIESYA
Sbjct: 901 IVGEWTHPYSREQAVYPVASLIDGKYWPPVGRVDNVFGDRNLVCACPSIESYA 953
Lambda K H
0.319 0.135 0.398
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: 2654
Number of extensions: 84
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: 953
Length of database: 953
Length adjustment: 44
Effective length of query: 909
Effective length of database: 909
Effective search space: 826281
Effective search space used: 826281
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 Pf6N2E2_5558 (Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2))
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.21428.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 1500.8 0.0 0 1500.7 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5558 Glycine dehydrogenase [decarboxy
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5558 Glycine dehydrogenase [decarboxylating] (glycine cleavage system P pro
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1500.7 0.0 0 0 1 939 [] 14 946 .. 14 946 .. 0.98
Alignments for each domain:
== domain 1 score: 1500.7 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkk 64
rh+Gp +++ + ml+ lG+d+l+al ++p++i+ + l ++ ++e +ala +k+ia+kn+
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5558 14 RHIGPRASDEQAMLERLGYDSLEALSASVIPESIKGTSVLDMGDGQSEADALASIKAIAAKNQL 77
9*************************************************************** PP
TIGR00461 65 vksyiGkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevan 128
+k+yiG+Gyy+ +p i+rnllenp wytaytpyqpeisqGrleallnfqt+++dltGl++an
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5558 78 FKTYIGQGYYNCHTPAPILRNLLENPAWYTAYTPYQPEISQGRLEALLNFQTLISDLTGLPIAN 141
**************************************************************** PP
TIGR00461 129 aslldegtaaaeamalsfrvskkk.ankfvvakdvhpqtlevvktraeplgievivddaskvkk 191
asllde+taaaeam +++r+sk+k +n+f+ + + hpqtl+v++traeplgi+v+v+d +++++
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5558 142 ASLLDEATAAAEAMTFCKRLSKNKgSNAFFASVHSHPQTLDVLRTRAEPLGIDVVVGDERELSD 205
************************99************************************** PP
TIGR00461 192 avdvlGvllqypatdGeildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqr 255
+G+llqypa++G+++dy++l+++ ++ +alv+vaadllaltlltppg++Gad+++Gsaqr
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5558 206 VSGFFGALLQYPASNGDLFDYRELTERFHTANALVAVAADLLALTLLTPPGEFGADVAIGSAQR 269
**************************************************************** PP
TIGR00461 256 fGvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqhirrdkatsnict 319
fGvplG+GGphaa+f++kd +kr +pGr+vGvs d+ G++alrla+qtreqhirr+katsnict
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5558 270 FGVPLGFGGPHAAYFSTKDAFKRDMPGRLVGVSVDRFGKPALRLAMQTREQHIRREKATSNICT 333
**************************************************************** PP
TIGR00461 320 aqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaa 383
aqvllan+as+yavyhGpkGl +ia+ri++lt+ila+gl +++++++ +fdtlt++ g ++a
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5558 334 AQVLLANIASMYAVYHGPKGLVQIANRIHHLTAILAKGLGALGLSVEQESFFDTLTLRTGAQTA 397
**************************************************************99 PP
TIGR00461 384 sevlkaaeeaeinlravvltevgialdetttkedvldllkvl..agkdnlgl.sseelsedvan 444
++ +a+++ inlr v+++ +g++ldett+++dv+ ll+++ ++ d +++ + l v++
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5558 398 -ALHDKARAQRINLRVVDAERLGLSLDETTSQADVEALLRLIgnLMADGKAVpDFAALAASVQS 460
.899999*******************************9986222334444327889******* PP
TIGR00461 445 sfpaellrddeilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpi 508
+pael r++ il ++vfnryhsetel+ryl +l kdlal+++miplGsctmklna+ em+p+
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5558 461 HIPAELVRQSAILSHPVFNRYHSETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPV 524
**************************************************************** PP
TIGR00461 509 twpefaeihpfapaeqveGykeliaqlekwlveitGfdaislqpnsGaqGeyaGlrvirsyhes 572
tw ef+ +hpfapaeq+ Gy++l +le+ l+ tG+da+slqpn+G+qGeyaGl +ir yh+s
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5558 525 TWAEFGALHPFAPAEQSAGYQQLTDELEAMLCAATGYDAVSLQPNAGSQGEYAGLLAIRAYHQS 588
**************************************************************** PP
TIGR00461 573 rgeehrniclipasahGtnpasaamaGlkvvpvkcdkeGnidlvdlkakaekagdelaavmvty 636
rge++r+iclip sahGtnpa+a+maG++vv+ +cd Gn+d++dl+aka ++ ++laa+m+ty
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5558 589 RGEDRRDICLIPSSAHGTNPATAHMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITY 652
**************************************************************** PP
TIGR00461 637 pstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlhktfsiphGGG 700
pst+Gvfee+ire++ i+h GGqvy+dGanmna vGl++pg++G dv+hlnlhktf+iphGGG
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5558 653 PSTHGVFEEGIREICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGG 716
**************************************************************** PP
TIGR00461 701 GpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGl 764
Gpg+gpigvkshlapflp+ ++++++gav aap+Gsasilpi++myi+mmG Gl
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5558 717 GPGVGPIGVKSHLAPFLPG--------HASMERKQGAVCAAPFGSASILPITWMYIRMMGGAGL 772
*******************........4578999****************************** PP
TIGR00461 765 kkasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGf 828
k+as++ailnany+a+rl+++y++l+ g+++ vahecildlr+lk+ +gi++ dvakrl+d+Gf
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5558 773 KRASQLAILNANYIARRLEEHYPVLYSGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGF 836
**************************************************************** PP
TIGR00461 829 haptlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqs 892
hapt+sfpvaGtlm+epteses+eeldrf+dami+i+eei av +G ++++dn+lknaph+
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5558 837 HAPTMSFPVAGTLMIEPTESESKEELDRFCDAMICIREEIRAVENGSLDKDDNPLKNAPHT-AA 899
************************************************************5.67 PP
TIGR00461 893 livaewadpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
+iv+ew++pysre+a+yp++ l k+wp v+r+d+++Gdrnlvc+c
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5558 900 EIVGEWTHPYSREQAVYPVASLIDGKYWPPVGRVDNVFGDRNLVCAC 946
89******************9999**********************9 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (953 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: 0.08u 0.03s 00:00:00.11 Elapsed: 00:00:00.10
# Mc/sec: 8.40
//
[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