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.649.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 0.00s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 8.50
//
[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:

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