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)
>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621
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.15733.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: 0.07u 0.02s 00:00:00.09 Elapsed: 00:00:00.09
# Mc/sec: 9.75
//
[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