GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Psychromonas ossibalaenae JAMM 0738

Align phosphoglucomutase; EC 5.4.2.2 (characterized)
to candidate WP_019614677.1 G327_RS0110225 alpha-D-glucose phosphate-specific phosphoglucomutase

Query= CharProtDB::CH_002452
         (546 letters)



>NCBI__GCF_000381745.1:WP_019614677.1
          Length = 550

 Score =  709 bits (1829), Expect = 0.0
 Identities = 348/543 (64%), Positives = 427/543 (78%), Gaps = 2/543 (0%)

Query: 1   MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPH 60
           MAIH RAG+ AQ SDL+++ +L + YY+  P+   A   V FGTSGHRG + +++F E H
Sbjct: 1   MAIHPRAGKTAQASDLVDIPKLVSAYYINIPDVSIASEQVAFGTSGHRGCSFKNAFTELH 60

Query: 61  ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120
           ILAI+QA+AE R + G TGP ++GKDTHALSEPAF S ++VL ANG+ VIVQ   G+TPT
Sbjct: 61  ILAISQALAEYRIEQGYTGPMFIGKDTHALSEPAFASAVQVLVANGIKVIVQAGGGYTPT 120

Query: 121 PAVSNAILVHNKKGGP-LADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANA 179
           P +S+AIL +N +    LADGIVITPSHNPPEDGG KYNPPNGGPAD++VTK+++DRAN 
Sbjct: 121 PVISHAILQYNNENPDNLADGIVITPSHNPPEDGGFKYNPPNGGPADSDVTKIIQDRANQ 180

Query: 180 LLADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGS 239
           +L D    +K+    EAM S  V+E D +QP+V+ L +++++ AI KAG+ +GVD LGGS
Sbjct: 181 ILDDQFDDIKQWDFSEAMESEFVEEYDYIQPYVDDLKNVLNVEAIAKAGIKIGVDTLGGS 240

Query: 240 GIEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDL 299
           G+ YW  I + Y L++ +VND+VD TF FM LDKDG IRMDCSS  AMAGL+ L+DKFD+
Sbjct: 241 GVAYWPVIAKTYGLDIEVVNDRVDPTFSFMTLDKDGKIRMDCSSPYAMAGLIELKDKFDV 300

Query: 300 AFANDPDYDRHGIVTPA-GLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRV 358
           A ANDPDYDRHGIVT + GL+NPNHYLAVAINYLF+HR  W +D  VGKTLVSS+MIDRV
Sbjct: 301 AIANDPDYDRHGIVTKSSGLLNPNHYLAVAINYLFKHRTDWPQDAIVGKTLVSSSMIDRV 360

Query: 359 VNDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLA 418
           V +L R++ EVPVGFKWFVDGL++G  GFGGEESAGASFLR DGT WSTDKDGII+ LLA
Sbjct: 361 VVELEREMSEVPVGFKWFVDGLYEGKLGFGGEESAGASFLRKDGTVWSTDKDGIILALLA 420

Query: 419 AEITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSASTLAGDPI 478
           AEI AVTGK+P EHY E  ++FG+P Y R  A AT  QKA L+ LSPEMV A TLAG+ I
Sbjct: 421 AEIIAVTGKDPGEHYAEFTEKFGSPIYQRFDAPATPEQKAVLANLSPEMVEAETLAGERI 480

Query: 479 TARLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEI 538
           TA+LT A GNGA+IGGLKV T+NGWFAARPSGTE+ YKIY ESF+G EH  +I+KEA EI
Sbjct: 481 TAKLTHASGNGAAIGGLKVTTENGWFAARPSGTENIYKIYSESFIGAEHIAEIQKEAQEI 540

Query: 539 VSE 541
           V++
Sbjct: 541 VAQ 543


Lambda     K      H
   0.316    0.134    0.395 

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: 936
Number of extensions: 37
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: 546
Length of database: 550
Length adjustment: 36
Effective length of query: 510
Effective length of database: 514
Effective search space:   262140
Effective search space used:   262140
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate WP_019614677.1 G327_RS0110225 (alpha-D-glucose phosphate-specific phosphoglucomutase)
to HMM TIGR01132 (pgm: phosphoglucomutase, alpha-D-glucose phosphate-specific (EC 5.4.2.2))

# 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/TIGR01132.hmm
# target sequence database:        /tmp/gapView.945789.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01132  [M=546]
Accession:   TIGR01132
Description: pgm: phosphoglucomutase, alpha-D-glucose phosphate-specific
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-284  930.4   0.7   1.7e-284  930.2   0.7    1.0  1  NCBI__GCF_000381745.1:WP_019614677.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000381745.1:WP_019614677.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  930.2   0.7  1.7e-284  1.7e-284       1     545 [.       1     545 [.       1     546 [. 1.00

  Alignments for each domain:
  == domain 1  score: 930.2 bits;  conditional E-value: 1.7e-284
                             TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevra 73 
                                           mai+praG+ aq++dl+d++klv++yy   pd   a+++v+fGtsGhrG++ k++f e hilai+qa++e+r 
  NCBI__GCF_000381745.1:WP_019614677.1   1 MAIHPRAGKTAQASDLVDIPKLVSAYYINIPDVSIASEQVAFGTSGHRGCSFKNAFTELHILAISQALAEYRI 73 
                                           89*********************************************************************** PP

                             TIGR01132  74 aqGitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGivitp 146
                                           +qG tGp++iGkdthalsepaf s+++vl+an+++vivq   +ytptp +shail yn+ + ++ladGivitp
  NCBI__GCF_000381745.1:WP_019614677.1  74 EQGYTGPMFIGKDTHALSEPAFASAVQVLVANGIKVIVQAGGGYTPTPVISHAILQYNNENPDNLADGIVITP 146
                                           ************************************************************************* PP

                             TIGR01132 147 shnppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladv 219
                                           shnppedGG+kynppnGGpa+++vtk+i+dran++l d+   +k+ d+++a++se v+e d+++pyvddl +v
  NCBI__GCF_000381745.1:WP_019614677.1 147 SHNPPEDGGFKYNPPNGGPADSDVTKIIQDRANQILDDQFDDIKQWDFSEAMESEFVEEYDYIQPYVDDLKNV 219
                                           ************************************************************************* PP

                             TIGR01132 220 vdlaairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagll 292
                                           ++++ai kag+++Gvd lGG+gv yw  ia++y+ld+ +vn+ vd+tf fmtldkdGkirmdcsspyamagl+
  NCBI__GCF_000381745.1:WP_019614677.1 220 LNVEAIAKAGIKIGVDTLGGSGVAYWPVIAKTYGLDIEVVNDRVDPTFSFMTLDKDGKIRMDCSSPYAMAGLI 292
                                           ************************************************************************* PP

                             TIGR01132 293 klkdkydlafgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlg 365
                                           +lkdk+d+a++nd+d+drhGivt ++Gllnpnhylavai+yl+khr +w+++  vGktlvss++idrvv +l+
  NCBI__GCF_000381745.1:WP_019614677.1 293 ELKDKFDVAIANDPDYDRHGIVTKSSGLLNPNHYLAVAINYLFKHRTDWPQDAIVGKTLVSSSMIDRVVVELE 365
                                           ************************************************************************* PP

                             TIGR01132 366 rklvevpvGfkwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydel 438
                                           r++ evpvGfkwfvdGl++g+lGfGGeesaGasflrkdGtvwstdkdGiilallaaei+avtGk+p+++y e+
  NCBI__GCF_000381745.1:WP_019614677.1 366 REMSEVPVGFKWFVDGLYEGKLGFGGEESAGASFLRKDGTVWSTDKDGIILALLAAEIIAVTGKDPGEHYAEF 438
                                           ************************************************************************* PP

                             TIGR01132 439 aakyGdpiyaridaaatsaqkarlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarps 511
                                           ++k+G+piy+r da+at++qka+l++lsp++v a+tlaG+ itaklt+a GngaaiGGlkvtt++gwfaarps
  NCBI__GCF_000381745.1:WP_019614677.1 439 TEKFGSPIYQRFDAPATPEQKAVLANLSPEMVEAETLAGERITAKLTHASGNGAAIGGLKVTTENGWFAARPS 511
                                           ************************************************************************* PP

                             TIGR01132 512 Gtedvykiyaesfkgeehlkeiekeaeeivdevl 545
                                           Gte++ykiy+esf g+eh+ ei+kea+eiv +++
  NCBI__GCF_000381745.1:WP_019614677.1 512 GTENIYKIYSESFIGAEHIAEIQKEAQEIVAQAF 545
                                           ******************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (550 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 34.97
//
[ok]

This GapMind analysis is from Sep 24 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:

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