GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gcvP in Dyella japonica UNC79MFTsu3.2

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)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_0055 N515DRAFT_0055 glycine
           dehydrogenase
          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.5303.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: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.09
# Mc/sec: 9.01
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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