Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate N515DRAFT_0055 N515DRAFT_0055 glycine dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1868
(950 letters)
>FitnessBrowser__Dyella79:N515DRAFT_0055
Length = 956
Score = 1254 bits (3244), Expect = 0.0
Identities = 622/939 (66%), Positives = 748/939 (79%), Gaps = 7/939 (0%)
Query: 12 FIARHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGLSEADALALIKS 71
FI RHIGP + ML+++G+DSLEA++ +++P IK + L L ++E +ALA I++
Sbjct: 18 FIERHIGPNDAEIAHMLSAIGYDSLEAMTDAIVPGQIKSAAPLALPPAMTEVEALAKIRA 77
Query: 72 IATKNQLFKTFIGQGYYGTHTPSPILRNLLENPAWYTAYTPYQPEISQGRLEALLNFQTL 131
IA KN++F++FIGQGYYGTHTP+ ILRN+LENPAWYTAYTPYQ EISQGR+EAL+NFQT+
Sbjct: 78 IADKNRVFRSFIGQGYYGTHTPNVILRNILENPAWYTAYTPYQAEISQGRMEALINFQTM 137
Query: 132 ISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASVHCHPQTLDVLRTRAEP 191
++DLTG+ I+NASLLDEATAA EAMT KR +K+K S+ FF + HPQTL+VLRTRA+
Sbjct: 138 VADLTGMDISNASLLDEATAAGEAMTLAKRSAKSK-SNVFFVADDVHPQTLEVLRTRADG 196
Query: 192 LGIDVVVGDERELTDVTPFFGALLQYPASNGDVFDYRELTERFHAANALVAVAADLLALT 251
+ I + VG + + V F G LLQYP + G + DYR + E HA ALVAVA DLLALT
Sbjct: 197 VDIALHVGPAADASTVDSF-GVLLQYPNTYGTIHDYRAVAEAVHARGALVAVATDLLALT 255
Query: 252 VLTAPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVGVSVDRFGNPA 311
++ APG +GAD+ IG++QRFGVP GFGGPHAAY + +DA+KR MPGRL+GVSVD G PA
Sbjct: 256 LIAAPGSWGADIVIGNSQRFGVPFGFGGPHAAYLACRDAYKRSMPGRLIGVSVDAEGKPA 315
Query: 312 LRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIANRVHHLTAILAK 371
RL +QTREQHIRREKATSNICTAQVLLA +ASMYAVYHGP GL +IA R H L AILA
Sbjct: 316 YRLTLQTREQHIRREKATSNICTAQVLLAVMASMYAVYHGPDGLQRIARRTHRLAAILAA 375
Query: 372 GLSALGLSVEQASFFDTLTVKAGAQTAALHDKAHAQRINLRVVDGERLGLSLDETTTQAD 431
L GL V FFDTL + G A+H KA + +NLR + G+ +G+SLDETTT+AD
Sbjct: 376 TLRKAGLEVG-GEFFDTLRI-TGVDADAIHAKAAGKGLNLRQIHGQCVGISLDETTTRAD 433
Query: 432 VETLWSLLSDGKALPDFAALAASVQSAIPATLVRQSPILSHPVFNRYHSETELMRYLRKL 491
V+ L L G L D + A+ A+PA L+RQ L HPVFN +HSE EL+RY+R L
Sbjct: 434 VQALAGLF--GAELSDIDEVDAATADALPAALLRQDAFLQHPVFNTHHSEHELLRYMRSL 491
Query: 492 ADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAGYQQLTDELEAM 551
ADKDLA+DRTMIPLGSCTMKLNA +EMIPVTW EFG +HP APA Q+ GY+QL DELEAM
Sbjct: 492 ADKDLAMDRTMIPLGSCTMKLNATAEMIPVTWPEFGNIHPLAPAAQTQGYKQLIDELEAM 551
Query: 552 LCAATGYDSVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIPSSAHGTNPATAQMA 611
L TGYD+VSLQPN+G+QGEYAGLLAIRAYH+SRG++ RD+CLIP SAHGTNPA+AQM
Sbjct: 552 LVECTGYDAVSLQPNSGAQGEYAGLLAIRAYHRSRGDEHRDVCLIPESAHGTNPASAQMC 611
Query: 612 GMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGIREICGIIHDNG 671
GM VVVT CDA GNVD+ED+RAKA ++ E LAALMITYPSTHGVFEE + IC I+H +G
Sbjct: 612 GMTVVVTKCDANGNVDLEDIRAKAEKYSERLAALMITYPSTHGVFEEDVVAICDIVHKHG 671
Query: 672 GQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKSHLAPFLP 731
GQVY DGANMNA+VGL PGK+G DVSHLNLHKTFCIPHGGGGPGVGP VKSHLAPFLP
Sbjct: 672 GQVYTDGANMNALVGLAKPGKWGSDVSHLNLHKTFCIPHGGGGPGVGPCAVKSHLAPFLP 731
Query: 732 GHAQMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAILNANYISRRLEEHY 791
E G V AA FGSASILPI+WMYI +MG GL++A+Q+A+LNANYI+RRL HY
Sbjct: 732 RTLGGEGSVGMVSAASFGSASILPISWMYITLMGQQGLRKATQVALLNANYIARRLASHY 791
Query: 792 PVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSFPVAGTLMIEPT 851
LYTG NGLVAHECILDLRPLKD++GIS +DVAKRLIDFGFHAPT+SFPVAGTLM+EPT
Sbjct: 792 ETLYTGRNGLVAHECILDLRPLKDATGISAEDVAKRLIDFGFHAPTLSFPVAGTLMVEPT 851
Query: 852 ESESKEELDRFCDAMIRIREEIRAVENGTLDKDDNPLKNAPHTAKELVG-EWSHPYSREQ 910
ESES+ ELDRF DAMI+IREEIRA+E+G LD++DNPLK+APHTA + G EW+H Y RE
Sbjct: 852 ESESQHELDRFIDAMIQIREEIRAIEDGRLDREDNPLKHAPHTANAVAGSEWTHAYPREL 911
Query: 911 AVYPVASLIEGKYWPPVGRVDNVFGDRNLVCACPSIESY 949
AV+P+ +L KYWPPV RVDNV+GD+N++CAC +++Y
Sbjct: 912 AVFPLPTLRLQKYWPPVARVDNVYGDKNVMCACIPVDAY 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: 2267
Number of extensions: 100
Number of successful extensions: 7
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: 956
Length adjustment: 44
Effective length of query: 906
Effective length of database: 912
Effective search space: 826272
Effective search space used: 826272
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 N515DRAFT_0055 N515DRAFT_0055 (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.1894.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 1475.3 0.1 0 1475.1 0.1 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_0055 N515DRAFT_0055 glycine dehydroge
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0055 N515DRAFT_0055 glycine dehydrogenase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1475.1 0.1 0 0 1 939 [] 21 944 .. 21 944 .. 0.99
Alignments for each domain:
== domain 1 score: 1475.1 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvk 66
rh+Gp++ae +ml ++G+d+l+a+++ +vp +i+ a pl l+ + +e eala++++ia+kn++++
lcl|FitnessBrowser__Dyella79:N515DRAFT_0055 21 RHIGPNDAEIAHMLSAIGYDSLEAMTDAIVPGQIKSAAPLALPPAMTEVEALAKIRAIADKNRVFR 86
9***************************************************************** PP
TIGR00461 67 syiGkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanasll 132
s+iG+Gyy+t +p vi+rn+lenp wytaytpyq+eisqGr+eal+nfqt+v dltG++++nasll
lcl|FitnessBrowser__Dyella79:N515DRAFT_0055 87 SFIGQGYYGTHTPNVILRNILENPAWYTAYTPYQAEISQGRMEALINFQTMVADLTGMDISNASLL 152
****************************************************************** PP
TIGR00461 133 degtaaaeamalsfrvskkkankfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGv 198
de+taa+eam l++r +k+k+n f+va+dvhpqtlev++tra+ ++i + v+ a + + +vd +Gv
lcl|FitnessBrowser__Dyella79:N515DRAFT_0055 153 DEATAAGEAMTLAKRSAKSKSNVFFVADDVHPQTLEVLRTRADGVDIALHVGPAADAS-TVDSFGV 217
****************************************************999976.6899*** PP
TIGR00461 199 llqypatdGeildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqrfGvplGyGG 264
llqyp t G+i+dy+a+ ++++ r alv+va+dllaltl+ +pg Gadiv+G +qrfGvp+G+GG
lcl|FitnessBrowser__Dyella79:N515DRAFT_0055 218 LLQYPNTYGTIHDYRAVAEAVHARGALVAVATDLLALTLIAAPGSWGADIVIGNSQRFGVPFGFGG 283
****************************************************************** PP
TIGR00461 265 phaaffavkdeykrklpGrivGvskdalGntalrlalqtreqhirrdkatsnictaqvllanvasl 330
phaa++a++d ykr++pGr++Gvs da G++a rl+lqtreqhirr+katsnictaqvlla++as+
lcl|FitnessBrowser__Dyella79:N515DRAFT_0055 284 PHAAYLACRDAYKRSMPGRLIGVSVDAEGKPAYRLTLQTREQHIRREKATSNICTAQVLLAVMASM 349
****************************************************************** PP
TIGR00461 331 yavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaasevlkaaeeaein 396
yavyhGp Gl++iarr +rl++ilaa+l++ ++e+ +fdtl++ + a + +a ++++n
lcl|FitnessBrowser__Dyella79:N515DRAFT_0055 350 YAVYHGPDGLQRIARRTHRLAAILAATLRKAGLEVG-GEFFDTLRITGVDADA--IHAKAAGKGLN 412
**********************************86.579*****99887666..99********* PP
TIGR00461 397 lravvltevgialdetttkedvldllkvlagkdnlglsseelsedvansfpaellrddeilrdevf 462
lr + + vgi+ldettt++dv+ l ++ ++ +++e++ a+++pa+llr+d +l+++vf
lcl|FitnessBrowser__Dyella79:N515DRAFT_0055 413 LRQIHGQCVGISLDETTTRADVQALAGLFGAEL---SDIDEVDAATADALPAALLRQDAFLQHPVF 475
***************************999854...699*************************** PP
TIGR00461 463 nryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGy 528
n++hse ellry+ +l kdla++++miplGsctmklnataem+p+twpef++ihp+apa q++Gy
lcl|FitnessBrowser__Dyella79:N515DRAFT_0055 476 NTHHSEHELLRYMRSLADKDLAMDRTMIPLGSCTMKLNATAEMIPVTWPEFGNIHPLAPAAQTQGY 541
****************************************************************** PP
TIGR00461 529 keliaqlekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpas 594
k+li +le+ lve tG+da+slqpnsGaqGeyaGl +ir yh srg+ehr++clip+sahGtnpas
lcl|FitnessBrowser__Dyella79:N515DRAFT_0055 542 KQLIDELEAMLVECTGYDAVSLQPNSGAQGEYAGLLAIRAYHRSRGDEHRDVCLIPESAHGTNPAS 607
****************************************************************** PP
TIGR00461 595 aamaGlkvvpvkcdkeGnidlvdlkakaekagdelaavmvtypstyGvfeetirevidivhrfGGq 660
a+m+G+ vv+ kcd +Gn+dl+d++akaek++++laa+m+typst+Gvfee + ++divh+ GGq
lcl|FitnessBrowser__Dyella79:N515DRAFT_0055 608 AQMCGMTVVVTKCDANGNVDLEDIRAKAEKYSERLAALMITYPSTHGVFEEDVVAICDIVHKHGGQ 673
****************************************************************** PP
TIGR00461 661 vyldGanmnaqvGltspgdlGadvchlnlhktfsiphGGGGpgmgpigvkshlapflpktdlvsvv 726
vy dGanmna vGl++pg+ G+dv+hlnlhktf+iphGGGGpg+gp +vkshlapflp+
lcl|FitnessBrowser__Dyella79:N515DRAFT_0055 674 VYTDGANMNALVGLAKPGKWGSDVSHLNLHKTFCIPHGGGGPGVGPCAVKSHLAPFLPR------- 732
***********************************************************....... PP
TIGR00461 727 elegesksigavsaapyGsasilpisymyikmmGaeGlkkasevailnanylakrlkdaykilfvg 792
+ g++ s+g+vsaa +Gsasilpis+myi +mG++Gl+ka++va+lnany+a+rl +y+ l++g
lcl|FitnessBrowser__Dyella79:N515DRAFT_0055 733 -TLGGEGSVGMVSAASFGSASILPISWMYITLMGQQGLRKATQVALLNANYIARRLASHYETLYTG 797
.5688899********************************************************** PP
TIGR00461 793 rdervahecildlrelkekagiealdvakrlldyGfhaptlsfpvaGtlmveptesesleeldrfi 858
r++ vahecildlr+lk+ +gi+a+dvakrl+d+GfhaptlsfpvaGtlmvepteses++eldrfi
lcl|FitnessBrowser__Dyella79:N515DRAFT_0055 798 RNGLVAHECILDLRPLKDATGISAEDVAKRLIDFGFHAPTLSFPVAGTLMVEPTESESQHELDRFI 863
****************************************************************** PP
TIGR00461 859 damiaikeeidavkaGeiklednilknaphslqslivaewadpysreeaaypapvlkyfkfwptva 924
dami i+eei a+ G+++ edn+lk aph+++ + +ew+++y re a++p+p l+ +k+wp va
lcl|FitnessBrowser__Dyella79:N515DRAFT_0055 864 DAMIQIREEIRAIEDGRLDREDNPLKHAPHTANAVAGSEWTHAYPRELAVFPLPTLRLQKYWPPVA 929
****************************************************************** PP
TIGR00461 925 rlddtyGdrnlvcsc 939
r+d++yGd+n++c+c
lcl|FitnessBrowser__Dyella79:N515DRAFT_0055 930 RVDNVYGDKNVMCAC 944
**************9 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (956 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: 0.04u 0.03s 00:00:00.07 Elapsed: 00:00:00.07
# Mc/sec: 12.72
//
[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