Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate Pf1N1B4_621 Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1868
(950 letters)
>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 Glycine dehydrogenase
[decarboxylating] (glycine cleavage system P protein)
(EC 1.4.4.2)
Length = 950
Score = 1838 bits (4760), Expect = 0.0
Identities = 915/950 (96%), Positives = 932/950 (98%)
Query: 1 MTQINLTTANEFIARHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGL 60
MTQINL TANEFIARHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGL
Sbjct: 1 MTQINLGTANEFIARHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGL 60
Query: 61 SEADALALIKSIATKNQLFKTFIGQGYYGTHTPSPILRNLLENPAWYTAYTPYQPEISQG 120
SEADALALIKSIA KNQLFKT+IGQGYYGTHTPSPILRNLLENPAWYTAYTPYQPEISQG
Sbjct: 61 SEADALALIKSIAGKNQLFKTYIGQGYYGTHTPSPILRNLLENPAWYTAYTPYQPEISQG 120
Query: 121 RLEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASVHCHPQ 180
RLEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASVHCHPQ
Sbjct: 121 RLEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASVHCHPQ 180
Query: 181 TLDVLRTRAEPLGIDVVVGDERELTDVTPFFGALLQYPASNGDVFDYRELTERFHAANAL 240
TLDVLRTRAEPLGIDVVVGDEREL DVTPFFGALLQYPASNGDVFDYRELTERFHAANAL
Sbjct: 181 TLDVLRTRAEPLGIDVVVGDERELADVTPFFGALLQYPASNGDVFDYRELTERFHAANAL 240
Query: 241 VAVAADLLALTVLTAPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLV 300
VAVAADLLALTVLT PGEFGADVAIGSAQRFGVPLGFGGPHAAYFST+DAFKRDMPGRLV
Sbjct: 241 VAVAADLLALTVLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTRDAFKRDMPGRLV 300
Query: 301 GVSVDRFGNPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIAN 360
GVSVDRFG PALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIA
Sbjct: 301 GVSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIAQ 360
Query: 361 RVHHLTAILAKGLSALGLSVEQASFFDTLTVKAGAQTAALHDKAHAQRINLRVVDGERLG 420
R+HHLTAILAKGLS+LGL+VEQA+FFDTLT+K G TA LHD+A AQ+INLRVVD ERLG
Sbjct: 361 RIHHLTAILAKGLSSLGLTVEQANFFDTLTIKTGVNTAKLHDQARAQQINLRVVDAERLG 420
Query: 421 LSLDETTTQADVETLWSLLSDGKALPDFAALAASVQSAIPATLVRQSPILSHPVFNRYHS 480
LSLDETT+QADVETLWS+LS+GKALPDFAALAASV+S +PA LVRQSPILSHPVFNRYHS
Sbjct: 421 LSLDETTSQADVETLWSVLSEGKALPDFAALAASVESTLPAALVRQSPILSHPVFNRYHS 480
Query: 481 ETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAG 540
ETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAG
Sbjct: 481 ETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAG 540
Query: 541 YQQLTDELEAMLCAATGYDSVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIPSSA 600
YQQLTDELEAMLCAATGYDS+SLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIPSSA
Sbjct: 541 YQQLTDELEAMLCAATGYDSISLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIPSSA 600
Query: 601 HGTNPATAQMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGI 660
HGTNPATA MAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGI
Sbjct: 601 HGTNPATANMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGI 660
Query: 661 REICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPI 720
REICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPI
Sbjct: 661 REICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPI 720
Query: 721 GVKSHLAPFLPGHAQMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAILNA 780
GVKSHL PFLPGHAQMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLK ASQLAILNA
Sbjct: 721 GVKSHLTPFLPGHAQMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKCASQLAILNA 780
Query: 781 NYISRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSF 840
NYISRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSF
Sbjct: 781 NYISRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSF 840
Query: 841 PVAGTLMIEPTESESKEELDRFCDAMIRIREEIRAVENGTLDKDDNPLKNAPHTAKELVG 900
PVAGTLMIEPTESESKEELDRFCDAMIRIREEIRAVENGTLDKDDNPLKNAPHTA E+VG
Sbjct: 841 PVAGTLMIEPTESESKEELDRFCDAMIRIREEIRAVENGTLDKDDNPLKNAPHTAAEIVG 900
Query: 901 EWSHPYSREQAVYPVASLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA 950
EW+HPYSREQAVYPVASLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA
Sbjct: 901 EWTHPYSREQAVYPVASLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA 950
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: 2638
Number of extensions: 97
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 Pf1N1B4_621 (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.2642.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 1497.2 0.0 0 1497.0 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 Glycine dehydrogenase [decarboxy
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 Glycine dehydrogenase [decarboxylating] (glycine cleavage system P prot
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1497.0 0.0 0 0 1 939 [] 15 943 .. 15 943 .. 0.99
Alignments for each domain:
== domain 1 score: 1497.0 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkv 65
rh+Gp + + + ml++lGfd+l+al ++p++i+ + l le +e +ala +k+ia kn+ +
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 15 RHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGLSEADALALIKSIAGKNQLF 79
9**************************************************************** PP
TIGR00461 66 ksyiGkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanas 130
k+yiG+Gyy+t +p i+rnllenp wytaytpyqpeisqGrleallnfqt+++dltGl++anas
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 80 KTYIGQGYYGTHTPSPILRNLLENPAWYTAYTPYQPEISQGRLEALLNFQTLISDLTGLPIANAS 144
***************************************************************** PP
TIGR00461 131 lldegtaaaeamalsfrvskkk.ankfvvakdvhpqtlevvktraeplgievivddaskvkkavd 194
llde+taaaeam +++r+sk+k + +f+ + ++hpqtl+v++traeplgi+v+v+d +++ + +
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 145 LLDEATAAAEAMTFCKRLSKNKgSHAFFASVHCHPQTLDVLRTRAEPLGIDVVVGDERELADVTP 209
**********************8999*************************************** PP
TIGR00461 195 vlGvllqypatdGeildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqrfGvp 259
+G+llqypa++G+++dy++l+++ + +alv+vaadllalt+ltppg++Gad+++GsaqrfGvp
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 210 FFGALLQYPASNGDVFDYRELTERFHAANALVAVAADLLALTVLTPPGEFGADVAIGSAQRFGVP 274
***************************************************************** PP
TIGR00461 260 lGyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqhirrdkatsnictaqvll 324
lG+GGphaa+f+++d +kr +pGr+vGvs d+ G++alrla+qtreqhirr+katsnictaqvll
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 275 LGFGGPHAAYFSTRDAFKRDMPGRLVGVSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLL 339
***************************************************************** PP
TIGR00461 325 anvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaasevlka 389
an+as+yavyhGpkGl +ia+ri++lt+ila+gl ++ ++++++fdtlt++ g ++a ++ +
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 340 ANIASMYAVYHGPKGLTQIAQRIHHLTAILAKGLSSLGLTVEQANFFDTLTIKTGVNTA-KLHDQ 403
*******************************************************9998.99*** PP
TIGR00461 390 aeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsedvansfpaellrdd 454
a++++inlr v+++ +g++ldett+++dv+ l+ vl+ + l+ + l v++++pa+l r++
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 404 ARAQQINLRVVDAERLGLSLDETTSQADVETLWSVLSEGKALP-DFAALAASVESTLPAALVRQS 467
************************************9866554.8899***************** PP
TIGR00461 455 eilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpf 519
il ++vfnryhsetel+ryl +l kdlal+++miplGsctmklna+ em+p+tw ef+ +hpf
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 468 PILSHPVFNRYHSETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPF 532
***************************************************************** PP
TIGR00461 520 apaeqveGykeliaqlekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclip 584
apaeq+ Gy++l +le+ l+ tG+d+islqpn+G+qGeyaGl +ir yh+srge++r+iclip
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 533 APAEQSAGYQQLTDELEAMLCAATGYDSISLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIP 597
***************************************************************** PP
TIGR00461 585 asahGtnpasaamaGlkvvpvkcdkeGnidlvdlkakaekagdelaavmvtypstyGvfeetire 649
sahGtnpa+a+maG++vv+ +cd Gn+d++dl+aka ++ ++laa+m+typst+Gvfee+ire
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 598 SSAHGTNPATANMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGIRE 662
***************************************************************** PP
TIGR00461 650 vidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlhktfsiphGGGGpgmgpigvkshla 714
++ i+h GGqvy+dGanmna vGl++pg++G dv+hlnlhktf+iphGGGGpg+gpigvkshl+
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 663 ICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKSHLT 727
***************************************************************** PP
TIGR00461 715 pflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlkkasevailnanyla 779
pflp++ ++++ gav aap+Gsasilpi++myi+mmG Glk as++ailnany+
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 728 PFLPGH--------AQMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKCASQLAILNANYIS 784
*****4........4567889******************************************** PP
TIGR00461 780 krlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptlsfpvaGtlmve 844
+rl+++y++l++g+++ vahecildlr+lk+ +gi++ dvakrl+d+Gfhapt+sfpvaGtlm+e
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 785 RRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSFPVAGTLMIE 849
***************************************************************** PP
TIGR00461 845 ptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaewadpysreeaay 909
pteses+eeldrf+dami i+eei av +G+++++dn+lknaph+ +iv+ew++pysre+a+y
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 850 PTESESKEELDRFCDAMIRIREEIRAVENGTLDKDDNPLKNAPHT-AAEIVGEWTHPYSREQAVY 913
********************************************5.6789*************** PP
TIGR00461 910 papvlkyfkfwptvarlddtyGdrnlvcsc 939
p++ l + k+wp v+r+d+++Gdrnlvc+c
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 914 PVASLIEGKYWPPVGRVDNVFGDRNLVCAC 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: 0.08u 0.03s 00:00:00.11 Elapsed: 00:00:00.10
# Mc/sec: 8.32
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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