Alignments for a candidate for pgmA in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Desulfovibrio vulgaris Hildenborough

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate 206872 DVU1428 phosphoglucomutase, alpha-D-glucose phosphate-specific

Query= BRENDA::A0A0H3NJ17
         (546 letters)



>MicrobesOnline__882:206872
          Length = 551

 Score =  659 bits (1699), Expect = 0.0
 Identities = 328/547 (59%), Positives = 406/547 (74%), Gaps = 1/547 (0%)

Query: 1   MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAGRHSFNEPH 60
           M++H  AG+      L+N+  L  +YY   P+    E  V FGTSGHRGS+   +FNE H
Sbjct: 1   MSVHPLAGERPSHDRLVNIPALMGEYYTGHPDTTAVERRVAFGTSGHRGSSLHGTFNEEH 60

Query: 61  ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120
           ILA+ QA+ + R ++GI GP ++G DTHALSE A  + LEVLAANGV+V +Q   GFTPT
Sbjct: 61  ILAVTQAVCDIRREDGIAGPLFLGMDTHALSECAHRTALEVLAANGVNVRLQTGGGFTPT 120

Query: 121 PAVSNAILVHNK-KGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANA 179
           P +S+AIL  N  +  P ADG+VITPSHNPPEDGG KYNPP+GGPADT VT+ +E RAN 
Sbjct: 121 PVISHAILCWNAHRDRPRADGVVITPSHNPPEDGGFKYNPPHGGPADTTVTRRIERRANE 180

Query: 180 LLAGGLQGVKRISLDAAMASGHVKAVDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGS 239
           LL  GL GV+R+ L  A+ +  ++AVDLV  +V  LA ++DM AI+ AGL +  DPLGGS
Sbjct: 181 LLDNGLAGVRRVVLHKALRTPGIEAVDLVSAYVNDLASVLDMDAIRGAGLRIAADPLGGS 240

Query: 240 GIEYWKRIAEHYKLNLTLVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDL 299
            + YW  IAE Y L++T+VN + D TFRFM  DKDG +RMDCSS  AM GL+ LR  +D+
Sbjct: 241 SLAYWDPIAEKYGLDITVVNREADPTFRFMPQDKDGKVRMDCSSPWAMRGLIDLRQSYDI 300

Query: 300 AFANDPDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPLWGKDVAVGKTLVSSAMIDRVV 359
           AF NDPD DRHGIVT  GL+NPNHY+A A+ YL++HRP W     +GKTLV+S+M+DRV 
Sbjct: 301 AFGNDPDADRHGIVTAQGLLNPNHYIAAAVWYLYRHRPGWNTTCGIGKTLVTSSMVDRVA 360

Query: 360 NDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAA 419
             LGRK+VEVPVGFKWFV  L DGS GFGGEESAGASFLR DGTPWSTDKDGIIM LLAA
Sbjct: 361 KLLGRKVVEVPVGFKWFVPLLLDGSCGFGGEESAGASFLRSDGTPWSTDKDGIIMNLLAA 420

Query: 420 EITAVTGKNPQEHYNELAARFGAPSYNRLQASATSAQKAALSKLSPEMVSASTLAGDPIT 479
           E+ AV  ++P E Y EL  R G P Y RLQ+ AT+AQ+A  + L+PE V A++LAG PIT
Sbjct: 421 EMMAVEERSPSEIYAELTERCGTPYYERLQSPATAAQRAVFAGLTPERVKATSLAGAPIT 480

Query: 480 ARLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEIV 539
           A LT APGNGA+IGGLKV+TD+GWFAARPSGTED YKIY ESF+  EH ++I+K+AV+IV
Sbjct: 481 AMLTHAPGNGAAIGGLKVVTDDGWFAARPSGTEDMYKIYTESFVSPEHLQRIQKDAVDIV 540

Query: 540 SEVLKNA 546
           + +  +A
Sbjct: 541 ASIFADA 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: 950
Number of extensions: 32
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: 551
Length adjustment: 36
Effective length of query: 510
Effective length of database: 515
Effective search space:   262650
Effective search space used:   262650
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 206872 DVU1428 (phosphoglucomutase, alpha-D-glucose phosphate-specific)
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.1309.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
     1e-263  861.6   0.0   1.2e-263  861.4   0.0    1.0  1  lcl|MicrobesOnline__882:206872  DVU1428 phosphoglucomutase, alph


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:206872  DVU1428 phosphoglucomutase, alpha-D-glucose phosphate-specific
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  861.4   0.0  1.2e-263  1.2e-263       1     545 [.       1     544 [.       1     545 [. 1.00

  Alignments for each domain:
  == domain 1  score: 861.4 bits;  conditional E-value: 1.2e-263
                       TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraaqGitG 79 
                                     m+++p+aG+++ ++ l+++++l+ +yy+ +pd+  ++++v+fGtsGhrGs+l+gtfne+hila++qav + r+++Gi+G
  lcl|MicrobesOnline__882:206872   1 MSVHPLAGERPSHDRLVNIPALMGEYYTGHPDTTAVERRVAFGTSGHRGSSLHGTFNEEHILAVTQAVCDIRREDGIAG 79 
                                     789**************************************************************************** PP

                       TIGR01132  80 plyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGivitpshnppedGGiky 158
                                     pl++G+dthalse a+ ++levlaan+v+v +q   ++tptp +shail +n  ++ ++adG+vitpshnppedGG+ky
  lcl|MicrobesOnline__882:206872  80 PLFLGMDTHALSECAHRTALEVLAANGVNVRLQTGGGFTPTPVISHAILCWNAHRDRPRADGVVITPSHNPPEDGGFKY 158
                                     ******************************************************************************* PP

                       TIGR01132 159 nppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvvdlaairkaglrlGvdpl 237
                                     npp+GGpa+t vt+ ie ranell ++l+gv+r+ l+kal++  ++++dlv+ yv+dla v+d++air aglr+ +dpl
  lcl|MicrobesOnline__882:206872 159 NPPHGGPADTTVTRRIERRANELLDNGLAGVRRVVLHKALRTPGIEAVDLVSAYVNDLASVLDMDAIRGAGLRIAADPL 237
                                     ******************************************************************************* PP

                       TIGR01132 238 GGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllklkdkydlafgndadadrhGivtp 316
                                     GG+++ yw++iaeky+ld+t+vn + d+tfrfm  dkdGk+rmdcssp am gl+ l++ yd+afgnd+dadrhGivt 
  lcl|MicrobesOnline__882:206872 238 GGSSLAYWDPIAEKYGLDITVVNREADPTFRFMPQDKDGKVRMDCSSPWAMRGLIDLRQSYDIAFGNDPDADRHGIVTA 316
                                     ******************************************************************************9 PP

                       TIGR01132 317 dkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgrklvevpvGfkwfvdGlldgslGfGGeesa 395
                                      +Gllnpnhy+a a++yly+hr++w+++  +Gktlv+s+++drv+  lgrk+vevpvGfkwfv  lldgs GfGGeesa
  lcl|MicrobesOnline__882:206872 317 -QGLLNPNHYIAAAVWYLYRHRPGWNTTCGIGKTLVTSSMVDRVAKLLGRKVVEVPVGFKWFVPLLLDGSCGFGGEESA 394
                                     .****************************************************************************** PP

                       TIGR01132 396 GasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaakyGdpiyaridaaatsaqkarlkklspdevsatt 474
                                     Gasflr dGt+wstdkdGii++llaae++av  ++p++ y el+++ G p+y+r++++at+aq+a+++ l+p++v at+
  lcl|MicrobesOnline__882:206872 395 GASFLRSDGTPWSTDKDGIIMNLLAAEMMAVEERSPSEIYAELTERCGTPYYERLQSPATAAQRAVFAGLTPERVKATS 473
                                     ******************************************************************************* PP

                       TIGR01132 475 laGdaitakltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfkgeehlkeiekeaeeivdevl 545
                                     laG +ita lt+apGngaaiGGlkv+td+gwfaarpsGted+ykiy+esf  +ehl++i+k+a +iv +++
  lcl|MicrobesOnline__882:206872 474 LAGAPITAMLTHAPGNGAAIGGLKVVTDDGWFAARPSGTEDMYKIYTESFVSPEHLQRIQKDAVDIVASIF 544
                                     *******************************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (551 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.47
//
[ok]

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

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Protein sequences (fasta format)
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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