Alignments for a candidate for pgmA in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Desulfovibrio vulgaris Miyazaki F

Align phosphoglucomutase; EC 5.4.2.2 (characterized)
to candidate 8499455 DvMF_0227 phosphoglucomutase (RefSeq)

Query= CharProtDB::CH_002452
         (546 letters)



>FitnessBrowser__Miya:8499455
          Length = 549

 Score =  686 bits (1771), Expect = 0.0
 Identities = 341/547 (62%), Positives = 416/547 (76%), Gaps = 1/547 (0%)

Query: 1   MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPH 60
           MA H +AGQ  + S L+++  L A YY   P+    E  V FGTSGHRG A   SFNE H
Sbjct: 1   MATHPQAGQRPEASQLVDIPALVAAYYTEHPDTAAPERRVSFGTSGHRGGALSGSFNEEH 60

Query: 61  ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120
           ILA+ QA+ E RA+ GITGP ++G DTHALSEPA  + LEVLAANGV  ++Q+  G+TPT
Sbjct: 61  ILAVTQAVCEYRAQAGITGPLFLGMDTHALSEPAHRTALEVLAANGVSTVIQQGGGYTPT 120

Query: 121 PAVSNAILVHNK-KGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANA 179
           P +S+AIL  N  +   L DGIVITPSHNPPEDGG KYNPP+GGPADT+ TK ++ RAN 
Sbjct: 121 PVISHAILTWNAGRAQGLGDGIVITPSHNPPEDGGFKYNPPHGGPADTDATKWIQRRANE 180

Query: 180 LLADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGS 239
           LL DG + V+R+ L +A+A+  V ++D V+ +V  LA +VDM AI+ AGL LG DPLGGS
Sbjct: 181 LLDDGNRAVRRMHLRDALAAPCVSQRDFVRGYVADLASVVDMPAIKAAGLKLGADPLGGS 240

Query: 240 GIEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDL 299
            + YW  I E Y L++T+VND VD TFRFM LDKDG IRMDCSS  AMAGL+ LRDKFD+
Sbjct: 241 SLAYWHPIAEAYGLDITVVNDAVDPTFRFMPLDKDGKIRMDCSSPWAMAGLINLRDKFDV 300

Query: 300 AFANDPDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRVV 359
           AF ND D DRHGIVT +GLMNPNHYLAVA+ YLF+HRPQW    AVGKTLV+S+M+DRV 
Sbjct: 301 AFGNDADADRHGIVTASGLMNPNHYLAVAVWYLFRHRPQWSPQCAVGKTLVTSSMVDRVA 360

Query: 360 NDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAA 419
             LGRK+VEVPVGFKWFV  L +GS GFGGEESAGASFLR DGT W+TDKDG+++ LLAA
Sbjct: 361 ASLGRKVVEVPVGFKWFVQPLLEGSCGFGGEESAGASFLRRDGTVWTTDKDGLLLNLLAA 420

Query: 420 EITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSASTLAGDPIT 479
           EI AV G++P E Y +L ++FGAP Y RLQ+ A + ++A L+ LSP++++A+ LAG PIT
Sbjct: 421 EIMAVEGRDPAELYTKLTEQFGAPLYERLQSPAGAERRAVLANLSPDVLTATELAGAPIT 480

Query: 480 ARLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEIV 539
           A LT APGN ASIGGLKV+TD+GWFAARPSGTED YKIY ESF G +H K+I++EAV+IV
Sbjct: 481 AMLTKAPGNDASIGGLKVITDDGWFAARPSGTEDMYKIYTESFKGSDHLKRIQQEAVDIV 540

Query: 540 SEVLKNA 546
                 A
Sbjct: 541 DRAFAAA 547


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: 899
Number of extensions: 42
Number of successful extensions: 2
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: 549
Length adjustment: 36
Effective length of query: 510
Effective length of database: 513
Effective search space:   261630
Effective search space used:   261630
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 8499455 DvMF_0227 (phosphoglucomutase (RefSeq))
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.14210.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.9e-282  923.4   0.0   2.1e-282  923.3   0.0    1.0  1  lcl|FitnessBrowser__Miya:8499455  DvMF_0227 phosphoglucomutase (Re


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8499455  DvMF_0227 phosphoglucomutase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  923.3   0.0  2.1e-282  2.1e-282       1     545 [.       1     544 [.       1     545 [. 1.00

  Alignments for each domain:
  == domain 1  score: 923.3 bits;  conditional E-value: 2.1e-282
                         TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraaqGi 77 
                                       ma +p+aGq++++++l+d+++lva+yy+ +pd+  ++++v+fGtsGhrG al g+fne+hila++qav e+ra+ Gi
  lcl|FitnessBrowser__Miya:8499455   1 MATHPQAGQRPEASQLVDIPALVAAYYTEHPDTAAPERRVSFGTSGHRGGALSGSFNEEHILAVTQAVCEYRAQAGI 77 
                                       789************************************************************************** PP

                         TIGR01132  78 tGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGivitpshnppedG 154
                                       tGpl++G+dthalsepa+ ++levlaan+v++++q+  +ytptp +shailt+n g+ ++l dGivitpshnppedG
  lcl|FitnessBrowser__Miya:8499455  78 TGPLFLGMDTHALSEPAHRTALEVLAANGVSTVIQQGGGYTPTPVISHAILTWNAGRAQGLGDGIVITPSHNPPEDG 154
                                       ***************************************************************************** PP

                         TIGR01132 155 GikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvvdlaairkaglr 231
                                       G+kynpp+GGpa+t++tk+i+ ranell d++++v+r++l  al++  v ++d+v+ yv+dla vvd+ ai+ agl+
  lcl|FitnessBrowser__Miya:8499455 155 GFKYNPPHGGPADTDATKWIQRRANELLDDGNRAVRRMHLRDALAAPCVSQRDFVRGYVADLASVVDMPAIKAAGLK 231
                                       ***************************************************************************** PP

                         TIGR01132 232 lGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllklkdkydlafgndada 308
                                       lG+dplGG+++ yw++iae+y+ld+t+vn+avd+tfrfm ldkdGkirmdcssp amagl++l+dk+d+afgndada
  lcl|FitnessBrowser__Miya:8499455 232 LGADPLGGSSLAYWHPIAEAYGLDITVVNDAVDPTFRFMPLDKDGKIRMDCSSPWAMAGLINLRDKFDVAFGNDADA 308
                                       ***************************************************************************** PP

                         TIGR01132 309 drhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgrklvevpvGfkwfvdGlldg 385
                                       drhGivt  +Gl+npnhylava++yl++hr+qw+ + avGktlv+s+++drv+a+lgrk+vevpvGfkwfv+ ll+g
  lcl|FitnessBrowser__Miya:8499455 309 DRHGIVTA-SGLMNPNHYLAVAVWYLFRHRPQWSPQCAVGKTLVTSSMVDRVAASLGRKVVEVPVGFKWFVQPLLEG 384
                                       *******9.9******************************************************************* PP

                         TIGR01132 386 slGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaakyGdpiyaridaaatsaqkarl 462
                                       s GfGGeesaGasflr+dGtvw+tdkdG++l+llaaei+av G++p + y +l++++G+p+y+r++++a ++++a+l
  lcl|FitnessBrowser__Miya:8499455 385 SCGFGGEESAGASFLRRDGTVWTTDKDGLLLNLLAAEIMAVEGRDPAELYTKLTEQFGAPLYERLQSPAGAERRAVL 461
                                       ***************************************************************************** PP

                         TIGR01132 463 kklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfkgeehlkeiekeaee 539
                                       ++lspd ++at+laG +ita ltkapGn+a+iGGlkv+td+gwfaarpsGted+ykiy+esfkg++hlk+i++ea +
  lcl|FitnessBrowser__Miya:8499455 462 ANLSPDVLTATELAGAPITAMLTKAPGNDASIGGLKVITDDGWFAARPSGTEDMYKIYTESFKGSDHLKRIQQEAVD 538
                                       ***************************************************************************** PP

                         TIGR01132 540 ivdevl 545
                                       ivd+++
  lcl|FitnessBrowser__Miya:8499455 539 IVDRAF 544
                                       ***986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (549 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.88
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources