Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate PfGW456L13_1868 Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1868
(950 letters)
>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1868
Length = 950
Score = 1894 bits (4907), Expect = 0.0
Identities = 950/950 (100%), Positives = 950/950 (100%)
Query: 1 MTQINLTTANEFIARHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGL 60
MTQINLTTANEFIARHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGL
Sbjct: 1 MTQINLTTANEFIARHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGL 60
Query: 61 SEADALALIKSIATKNQLFKTFIGQGYYGTHTPSPILRNLLENPAWYTAYTPYQPEISQG 120
SEADALALIKSIATKNQLFKTFIGQGYYGTHTPSPILRNLLENPAWYTAYTPYQPEISQG
Sbjct: 61 SEADALALIKSIATKNQLFKTFIGQGYYGTHTPSPILRNLLENPAWYTAYTPYQPEISQG 120
Query: 121 RLEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASVHCHPQ 180
RLEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASVHCHPQ
Sbjct: 121 RLEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASVHCHPQ 180
Query: 181 TLDVLRTRAEPLGIDVVVGDERELTDVTPFFGALLQYPASNGDVFDYRELTERFHAANAL 240
TLDVLRTRAEPLGIDVVVGDERELTDVTPFFGALLQYPASNGDVFDYRELTERFHAANAL
Sbjct: 181 TLDVLRTRAEPLGIDVVVGDERELTDVTPFFGALLQYPASNGDVFDYRELTERFHAANAL 240
Query: 241 VAVAADLLALTVLTAPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLV 300
VAVAADLLALTVLTAPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLV
Sbjct: 241 VAVAADLLALTVLTAPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLV 300
Query: 301 GVSVDRFGNPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIAN 360
GVSVDRFGNPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIAN
Sbjct: 301 GVSVDRFGNPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIAN 360
Query: 361 RVHHLTAILAKGLSALGLSVEQASFFDTLTVKAGAQTAALHDKAHAQRINLRVVDGERLG 420
RVHHLTAILAKGLSALGLSVEQASFFDTLTVKAGAQTAALHDKAHAQRINLRVVDGERLG
Sbjct: 361 RVHHLTAILAKGLSALGLSVEQASFFDTLTVKAGAQTAALHDKAHAQRINLRVVDGERLG 420
Query: 421 LSLDETTTQADVETLWSLLSDGKALPDFAALAASVQSAIPATLVRQSPILSHPVFNRYHS 480
LSLDETTTQADVETLWSLLSDGKALPDFAALAASVQSAIPATLVRQSPILSHPVFNRYHS
Sbjct: 421 LSLDETTTQADVETLWSLLSDGKALPDFAALAASVQSAIPATLVRQSPILSHPVFNRYHS 480
Query: 481 ETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAG 540
ETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAG
Sbjct: 481 ETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAG 540
Query: 541 YQQLTDELEAMLCAATGYDSVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIPSSA 600
YQQLTDELEAMLCAATGYDSVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIPSSA
Sbjct: 541 YQQLTDELEAMLCAATGYDSVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIPSSA 600
Query: 601 HGTNPATAQMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGI 660
HGTNPATAQMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGI
Sbjct: 601 HGTNPATAQMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGI 660
Query: 661 REICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPI 720
REICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPI
Sbjct: 661 REICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPI 720
Query: 721 GVKSHLAPFLPGHAQMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAILNA 780
GVKSHLAPFLPGHAQMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAILNA
Sbjct: 721 GVKSHLAPFLPGHAQMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAILNA 780
Query: 781 NYISRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSF 840
NYISRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSF
Sbjct: 781 NYISRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSF 840
Query: 841 PVAGTLMIEPTESESKEELDRFCDAMIRIREEIRAVENGTLDKDDNPLKNAPHTAKELVG 900
PVAGTLMIEPTESESKEELDRFCDAMIRIREEIRAVENGTLDKDDNPLKNAPHTAKELVG
Sbjct: 841 PVAGTLMIEPTESESKEELDRFCDAMIRIREEIRAVENGTLDKDDNPLKNAPHTAKELVG 900
Query: 901 EWSHPYSREQAVYPVASLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA 950
EWSHPYSREQAVYPVASLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA
Sbjct: 901 EWSHPYSREQAVYPVASLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA 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: 2668
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 PfGW456L13_1868 (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.9602.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 1499.8 0.0 0 1499.7 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1868 Glycine dehydrogenase [decarboxy
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1868 Glycine dehydrogenase [decarboxylating] (glycine cleavage sys
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1499.7 0.0 0 0 1 939 [] 15 943 .. 15 943 .. 0.99
Alignments for each domain:
== domain 1 score: 1499.7 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealael 55
rh+Gp + + + ml++lGfd+l+al ++p++i+ + l le +e +ala +
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1868 15 RHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGLSEADALALI 69
9****************************************************** PP
TIGR00461 56 kkiasknkkvksyiGkGyyatilppviqrnllenpgwytaytpyqpeisqGrlea 110
k+ia+kn+ +k++iG+Gyy+t +p i+rnllenp wytaytpyqpeisqGrlea
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1868 70 KSIATKNQLFKTFIGQGYYGTHTPSPILRNLLENPAWYTAYTPYQPEISQGRLEA 124
******************************************************* PP
TIGR00461 111 llnfqtvvldltGlevanaslldegtaaaeamalsfrvskkk.ankfvvakdvhp 164
llnfqt+++dltGl++anasllde+taaaeam +++r+sk+k + +f+ + ++hp
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1868 125 LLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKgSHAFFASVHCHP 179
******************************************8999********* PP
TIGR00461 165 qtlevvktraeplgievivddaskvkkavdvlGvllqypatdGeildykalidel 219
qtl+v++traeplgi+v+v+d +++++ + +G+llqypa++G+++dy++l+++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1868 180 QTLDVLRTRAEPLGIDVVVGDERELTDVTPFFGALLQYPASNGDVFDYRELTERF 234
******************************************************* PP
TIGR00461 220 ksrkalvsvaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkd 274
+ +alv+vaadllalt+lt+pg++Gad+++GsaqrfGvplG+GGphaa+f++kd
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1868 235 HAANALVAVAADLLALTVLTAPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKD 289
******************************************************* PP
TIGR00461 275 eykrklpGrivGvskdalGntalrlalqtreqhirrdkatsnictaqvllanvas 329
+kr +pGr+vGvs d+ Gn+alrla+qtreqhirr+katsnictaqvllan+as
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1868 290 AFKRDMPGRLVGVSVDRFGNPALRLAMQTREQHIRREKATSNICTAQVLLANIAS 344
******************************************************* PP
TIGR00461 330 lyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaas 384
+yavyhGpkGl +ia+r+++lt+ila+gl +++++++ +fdtltv+ g ++a
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1868 345 MYAVYHGPKGLTQIANRVHHLTAILAKGLSALGLSVEQASFFDTLTVKAGAQTA- 398
***************************************************999. PP
TIGR00461 385 evlkaaeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseels 439
++ +a+++ inlr v+ + +g++ldettt++dv+ l+ +l+ + l+ + l
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1868 399 ALHDKAHAQRINLRVVDGERLGLSLDETTTQADVETLWSLLSDGKALP-DFAALA 452
899999*********************************998755444.8899** PP
TIGR00461 440 edvansfpaellrddeilrdevfnryhsetellrylhrleskdlalnqsmiplGs 494
v++++pa l r++ il ++vfnryhsetel+ryl +l kdlal+++miplGs
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1868 453 ASVQSAIPATLVRQSPILSHPVFNRYHSETELMRYLRKLADKDLALDRTMIPLGS 507
******************************************************* PP
TIGR00461 495 ctmklnataemlpitwpefaeihpfapaeqveGykeliaqlekwlveitGfdais 549
ctmklna+ em+p+tw ef+ +hpfapaeq+ Gy++l +le+ l+ tG+d++s
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1868 508 CTMKLNAASEMIPVTWAEFGALHPFAPAEQSAGYQQLTDELEAMLCAATGYDSVS 562
******************************************************* PP
TIGR00461 550 lqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvp 604
lqpn+G+qGeyaGl +ir yh+srge++r+iclip sahGtnpa+a+maG++vv+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1868 563 LQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIPSSAHGTNPATAQMAGMRVVV 617
******************************************************* PP
TIGR00461 605 vkcdkeGnidlvdlkakaekagdelaavmvtypstyGvfeetirevidivhrfGG 659
+cd Gn+d++dl+aka ++ ++laa+m+typst+Gvfee+ire++ i+h GG
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1868 618 TACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGIREICGIIHDNGG 672
******************************************************* PP
TIGR00461 660 qvyldGanmnaqvGltspgdlGadvchlnlhktfsiphGGGGpgmgpigvkshla 714
qvy+dGanmna vGl++pg++G dv+hlnlhktf+iphGGGGpg+gpigvkshla
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1868 673 QVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKSHLA 727
******************************************************* PP
TIGR00461 715 pflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlkkase 769
pflp++ ++++ gav aap+Gsasilpi++myi+mmG Glk+as+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1868 728 PFLPGH--------AQMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQ 774
*****4........4567889********************************** PP
TIGR00461 770 vailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrll 824
+ailnany+ +rl+++y++l++g+++ vahecildlr+lk+ +gi++ dvakrl+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1868 775 LAILNANYISRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLI 829
******************************************************* PP
TIGR00461 825 dyGfhaptlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeikle 879
d+Gfhapt+sfpvaGtlm+epteses+eeldrf+dami i+eei av +G+++++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1868 830 DFGFHAPTMSFPVAGTLMIEPTESESKEELDRFCDAMIRIREEIRAVENGTLDKD 884
******************************************************* PP
TIGR00461 880 dnilknaphslqslivaewadpysreeaaypapvlkyfkfwptvarlddtyGdrn 934
dn+lknaph++ +++v+ew +pysre+a+yp++ l + k+wp v+r+d+++Gdrn
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1868 885 DNPLKNAPHTA-KELVGEWSHPYSREQAVYPVASLIEGKYWPPVGRVDNVFGDRN 938
*********76.5689*************************************** PP
TIGR00461 935 lvcsc 939
lvc+c
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1868 939 LVCAC 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 0.03s 00:00:00.10 Elapsed: 00:00:00.09
# Mc/sec: 9.03
//
[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