Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate GFF4367 PS417_22360 glycine dehydrogenase
Query= reanno::WCS417:GFF4367
(946 letters)
>FitnessBrowser__WCS417:GFF4367
Length = 946
Score = 1890 bits (4896), Expect = 0.0
Identities = 946/946 (100%), Positives = 946/946 (100%)
Query: 1 MTVQLTTANEFIARHIGPRQEDEQQMLASLGFDSLEALSASVIPESIKGTSVLGLEDGLS 60
MTVQLTTANEFIARHIGPRQEDEQQMLASLGFDSLEALSASVIPESIKGTSVLGLEDGLS
Sbjct: 1 MTVQLTTANEFIARHIGPRQEDEQQMLASLGFDSLEALSASVIPESIKGTSVLGLEDGLS 60
Query: 61 EAEALAKIKAIAGKNQLFKTYIGQGYYNCHTPSPILRNLLENPAWYTAYTPYQPEISQGR 120
EAEALAKIKAIAGKNQLFKTYIGQGYYNCHTPSPILRNLLENPAWYTAYTPYQPEISQGR
Sbjct: 61 EAEALAKIKAIAGKNQLFKTYIGQGYYNCHTPSPILRNLLENPAWYTAYTPYQPEISQGR 120
Query: 121 LEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSNAFFASIHSHPQT 180
LEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSNAFFASIHSHPQT
Sbjct: 121 LEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSNAFFASIHSHPQT 180
Query: 181 LDVLRTRAEPLGIDVVVGDERELTDVSPFFGALLQYPASNGDVFDYRELTERFHAAHGLV 240
LDVLRTRAEPLGIDVVVGDERELTDVSPFFGALLQYPASNGDVFDYRELTERFHAAHGLV
Sbjct: 181 LDVLRTRAEPLGIDVVVGDERELTDVSPFFGALLQYPASNGDVFDYRELTERFHAAHGLV 240
Query: 241 AVAADLLALTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVG 300
AVAADLLALTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVG
Sbjct: 241 AVAADLLALTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVG 300
Query: 301 VSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIARR 360
VSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIARR
Sbjct: 301 VSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIARR 360
Query: 361 VHQLTAILAKGLTALGQNVEQAHFFDTLTLNTGANTAAVHDKARAQRINLRVVDAERVGV 420
VHQLTAILAKGLTALGQNVEQAHFFDTLTLNTGANTAAVHDKARAQRINLRVVDAERVGV
Sbjct: 361 VHQLTAILAKGLTALGQNVEQAHFFDTLTLNTGANTAAVHDKARAQRINLRVVDAERVGV 420
Query: 421 SVDETTTQADIETLWAIFADGKALPDFAAQVESTLPAALLRQSPVLSHPVFNRYHSETEL 480
SVDETTTQADIETLWAIFADGKALPDFAAQVESTLPAALLRQSPVLSHPVFNRYHSETEL
Sbjct: 421 SVDETTTQADIETLWAIFADGKALPDFAAQVESTLPAALLRQSPVLSHPVFNRYHSETEL 480
Query: 481 MRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAGYLEL 540
MRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAGYLEL
Sbjct: 481 MRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAGYLEL 540
Query: 541 TSDLEAMLCAATGYDAISLQPNAGSQGEYAGLLAIRAYHQSRGDERRDICLIPSSAHGTN 600
TSDLEAMLCAATGYDAISLQPNAGSQGEYAGLLAIRAYHQSRGDERRDICLIPSSAHGTN
Sbjct: 541 TSDLEAMLCAATGYDAISLQPNAGSQGEYAGLLAIRAYHQSRGDERRDICLIPSSAHGTN 600
Query: 601 PATANMAGMRVVVTACDARGNVDIEDLRAKAIEHRDHLAALMITYPSTHGVFEEGIREIC 660
PATANMAGMRVVVTACDARGNVDIEDLRAKAIEHRDHLAALMITYPSTHGVFEEGIREIC
Sbjct: 601 PATANMAGMRVVVTACDARGNVDIEDLRAKAIEHRDHLAALMITYPSTHGVFEEGIREIC 660
Query: 661 GIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKS 720
GIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKS
Sbjct: 661 GIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKS 720
Query: 721 HLTPFLPGHAAMERKEGAVCAAPFGSASILPITWMYISMMGGAGLKRASQLAILNANYIS 780
HLTPFLPGHAAMERKEGAVCAAPFGSASILPITWMYISMMGGAGLKRASQLAILNANYIS
Sbjct: 721 HLTPFLPGHAAMERKEGAVCAAPFGSASILPITWMYISMMGGAGLKRASQLAILNANYIS 780
Query: 781 RRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSFPVAG 840
RRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSFPVAG
Sbjct: 781 RRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSFPVAG 840
Query: 841 TLMIEPTESESKEELDRFCNAMIAIREEIRAVENGTLDKDDNPLKNAPHTAAELVSEWTH 900
TLMIEPTESESKEELDRFCNAMIAIREEIRAVENGTLDKDDNPLKNAPHTAAELVSEWTH
Sbjct: 841 TLMIEPTESESKEELDRFCNAMIAIREEIRAVENGTLDKDDNPLKNAPHTAAELVSEWTH 900
Query: 901 PYTREQAVYPVPSLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA 946
PYTREQAVYPVPSLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA
Sbjct: 901 PYTREQAVYPVPSLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA 946
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: 2509
Number of extensions: 77
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: 946
Length of database: 946
Length adjustment: 44
Effective length of query: 902
Effective length of database: 902
Effective search space: 813604
Effective search space used: 813604
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 GFF4367 PS417_22360 (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.6950.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 1495.4 0.0 0 1495.2 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF4367 PS417_22360 glycine dehydrogenas
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4367 PS417_22360 glycine dehydrogenase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1495.2 0.0 0 0 1 939 [] 14 939 .. 14 939 .. 0.99
Alignments for each domain:
== domain 1 score: 1495.2 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyiGkGyya 75
rh+Gp + + ++ml +lGfd+l+al ++p++i+ + l le +e eala++k+ia kn+ +k+yiG+Gyy+
lcl|FitnessBrowser__WCS417:GFF4367 14 RHIGPRQEDEQQMLASLGFDSLEALSASVIPESIKGTSVLGLEDGLSEAEALAKIKAIAGKNQLFKTYIGQGYYN 88
9************************************************************************** PP
TIGR00461 76 tilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaaaeamalsfrvsk 150
+p i+rnllenp wytaytpyqpeisqGrleallnfqt+++dltGl++anasllde+taaaeam +++r+sk
lcl|FitnessBrowser__WCS417:GFF4367 89 CHTPSPILRNLLENPAWYTAYTPYQPEISQGRLEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSK 163
*************************************************************************** PP
TIGR00461 151 kk.ankfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdGeildykalidelksrka 224
+k +n+f+ + + hpqtl+v++traeplgi+v+v+d +++++ +G+llqypa++G+++dy++l+++ + +
lcl|FitnessBrowser__WCS417:GFF4367 164 NKgSNAFFASIHSHPQTLDVLRTRAEPLGIDVVVGDERELTDVSPFFGALLQYPASNGDVFDYRELTERFHAAHG 238
**99*********************************************************************** PP
TIGR00461 225 lvsvaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrl 299
lv+vaadllaltlltppg++Gad+++GsaqrfGvplG+GGphaa+f++kd +kr +pGr+vGvs d+ G++alrl
lcl|FitnessBrowser__WCS417:GFF4367 239 LVAVAADLLALTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVGVSVDRFGKPALRL 313
*************************************************************************** PP
TIGR00461 300 alqtreqhirrdkatsnictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtl 374
a+qtreqhirr+katsnictaqvllan+as+yavyhGpkGl +iarr+++lt+ila+gl + +++++++fdtl
lcl|FitnessBrowser__WCS417:GFF4367 314 AMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIARRVHQLTAILAKGLTALGQNVEQAHFFDTL 388
*************************************************************************** PP
TIGR00461 375 tvevgekaasevlkaaeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsedvansfpae 449
t++ g ++a +v +a+++ inlr v+++ vg+++dettt++d++ l+ ++a + + + +v++++pa+
lcl|FitnessBrowser__WCS417:GFF4367 389 TLNTGANTA-AVHDKARAQRINLRVVDAERVGVSVDETTTQADIETLWAIFADGK----ALPDFAAQVESTLPAA 458
*****9998.899999***********************************9855....4556788999****** PP
TIGR00461 450 llrddeilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeq 524
llr++ +l ++vfnryhsetel+ryl +l kdlal+++miplGsctmklna+ em+p+tw ef+ +hpfapaeq
lcl|FitnessBrowser__WCS417:GFF4367 459 LLRQSPVLSHPVFNRYHSETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQ 533
*************************************************************************** PP
TIGR00461 525 veGykeliaqlekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaG 599
+ Gy el ++le+ l+ tG+daislqpn+G+qGeyaGl +ir yh+srg+e+r+iclip sahGtnpa+a+maG
lcl|FitnessBrowser__WCS417:GFF4367 534 SAGYLELTSDLEAMLCAATGYDAISLQPNAGSQGEYAGLLAIRAYHQSRGDERRDICLIPSSAHGTNPATANMAG 608
*************************************************************************** PP
TIGR00461 600 lkvvpvkcdkeGnidlvdlkakaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGl 674
++vv+ +cd Gn+d++dl+aka ++ d+laa+m+typst+Gvfee+ire++ i+h GGqvy+dGanmna vGl
lcl|FitnessBrowser__WCS417:GFF4367 609 MRVVVTACDARGNVDIEDLRAKAIEHRDHLAALMITYPSTHGVFEEGIREICGIIHDNGGQVYIDGANMNAMVGL 683
*************************************************************************** PP
TIGR00461 675 tspgdlGadvchlnlhktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasil 749
++pg++G dv+hlnlhktf+iphGGGGpg+gpigvkshl+pflp+ +++++ gav aap+Gsasil
lcl|FitnessBrowser__WCS417:GFF4367 684 CAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKSHLTPFLPG--------HAAMERKEGAVCAAPFGSASIL 750
*********************************************........4688999*************** PP
TIGR00461 750 pisymyikmmGaeGlkkasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrll 824
pi++myi mmG Glk+as++ailnany+ +rl+++y++l++g+++ vahecildlr+lk+ +gi++ dvakrl+
lcl|FitnessBrowser__WCS417:GFF4367 751 PITWMYISMMGGAGLKRASQLAILNANYISRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLI 825
*************************************************************************** PP
TIGR00461 825 dyGfhaptlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaewa 899
d+Gfhapt+sfpvaGtlm+epteses+eeldrf++amiai+eei av +G+++++dn+lknaph++ ++v+ew+
lcl|FitnessBrowser__WCS417:GFF4367 826 DFGFHAPTMSFPVAGTLMIEPTESESKEELDRFCNAMIAIREEIRAVENGTLDKDDNPLKNAPHTA-AELVSEWT 899
****************************************************************65.6789**** PP
TIGR00461 900 dpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
+py+re+a+yp+p l + k+wp v+r+d+++Gdrnlvc+c
lcl|FitnessBrowser__WCS417:GFF4367 900 HPYTREQAVYPVPSLIEGKYWPPVGRVDNVFGDRNLVCAC 939
***************************************9 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (946 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 0.04s 00:00:00.12 Elapsed: 00:00:00.10
# Mc/sec: 8.17
//
[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