Alignments for a candidate for pgmA in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Shewanella amazonensis SB2B

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate 6937550 Sama_1706 phosphoglucomutase (RefSeq)

Query= BRENDA::A0A0H3NJ17
         (546 letters)



>FitnessBrowser__SB2B:6937550
          Length = 560

 Score =  648 bits (1671), Expect = 0.0
 Identities = 322/549 (58%), Positives = 401/549 (73%), Gaps = 5/549 (0%)

Query: 1   MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAGRHSFNEPH 60
           MAIH+RAG+ AQQ DL+N+ +L + YY L P+A +    V FGTSGHRG A   SFNE H
Sbjct: 1   MAIHDRAGKQAQQGDLVNIPKLMSHYYRLLPDASDPAQKVSFGTSGHRGCAFHRSFNEQH 60

Query: 61  ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120
           ILAIAQA+ + R +  ITGP Y+G DTHALS+ A++SV+EVL AN V V+ Q ++ +TPT
Sbjct: 61  ILAIAQAVVDWRTQADITGPLYLGMDTHALSQAAYLSVIEVLIANKVQVLAQRDDAYTPT 120

Query: 121 PAVSNAILVHNK----KGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDR 176
           P VS AI+  N+    +   L+DGI+ITPSHNPP+DGGIKYNPP+GGPA+ ++T  +E R
Sbjct: 121 PVVSQAIVAANRHQTGEDALLSDGIIITPSHNPPQDGGIKYNPPHGGPAEGDITSWIETR 180

Query: 177 ANALLAGGLQGVKRISLDAAMASGHVKAVDLVQPFVEGLADIVDMAAIQKAGLTLGVDPL 236
           AN  LA GL GV+R++   A     +K VDL+ P+V+ LA+++DMAAI KAG+ +GVDPL
Sbjct: 181 ANHYLAHGLDGVRRVNYGIASGLSLLKHVDLISPYVQSLAEVIDMAAIAKAGVRMGVDPL 240

Query: 237 GGSGIEYWKRIAEHYKLNLTLVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDK 296
           GGSGI YW+ IAEHY LN+ +VN  +D TF FM LDKDG IRMDCSS  AMAGLL  +D+
Sbjct: 241 GGSGIHYWQPIAEHYGLNIEVVNQAIDPTFDFMPLDKDGKIRMDCSSPYAMAGLLVHKDE 300

Query: 297 FDLAFANDPDYDRHGIVTP-AGLMNPNHYLAVAINYLFQHRPLWGKDVAVGKTLVSSAMI 355
           FD+   NDPDYDRHGIV P +GLM+PNHYLAVAI+YL  HRP W K +AVGKTLVSSA+I
Sbjct: 301 FDICVGNDPDYDRHGIVCPGSGLMDPNHYLAVAIDYLLGHRPNWAKTLAVGKTLVSSALI 360

Query: 356 DRVVNDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMC 415
           D+V    G  L+EVPVGFKWFVDGL D S  FGGEESAGA+FL+ DG+ W TDKDG I+ 
Sbjct: 361 DKVCMAHGVPLMEVPVGFKWFVDGLADSSVCFGGEESAGAAFLKMDGSTWCTDKDGFILA 420

Query: 416 LLAAEITAVTGKNPQEHYNELAARFGAPSYNRLQASATSAQKAALSKLSPEMVSASTLAG 475
           LLAAEI AVTGK P E Y EL A  G   Y R+ +      KA    L+ + + A+++AG
Sbjct: 421 LLAAEILAVTGKTPAERYEELVAEHGRSFYKRIDSPLNPKMKAKFGALNAQTLGATSVAG 480

Query: 476 DPITARLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEA 535
           D ITA LT APGNGA+IGG+KV TD GWFAARPSGTE  +K+Y ESF+ E H  ++  +A
Sbjct: 481 DAITAVLTKAPGNGAAIGGIKVCTDKGWFAARPSGTEPLFKLYAESFVSEAHLGELISDA 540

Query: 536 VEIVSEVLK 544
             ++   LK
Sbjct: 541 QSLLGTALK 549


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: 913
Number of extensions: 31
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: 560
Length adjustment: 36
Effective length of query: 510
Effective length of database: 524
Effective search space:   267240
Effective search space used:   267240
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 6937550 Sama_1706 (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.20426.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.2e-260  849.1   0.1     7e-260  848.9   0.1    1.0  1  lcl|FitnessBrowser__SB2B:6937550  Sama_1706 phosphoglucomutase (Re


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937550  Sama_1706 phosphoglucomutase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  848.9   0.1    7e-260    7e-260       1     545 [.       1     548 [.       1     549 [. 0.98

  Alignments for each domain:
  == domain 1  score: 848.9 bits;  conditional E-value: 7e-260
                         TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraaqGi 77 
                                       mai++raG++aqq dl++++kl+++yy+l pda ++aqkv+fGtsGhrG+a + +fne+hilaiaqavv+ r++  i
  lcl|FitnessBrowser__SB2B:6937550   1 MAIHDRAGKQAQQGDLVNIPKLMSHYYRLLPDASDPAQKVSFGTSGHRGCAFHRSFNEQHILAIAQAVVDWRTQADI 77 
                                       89*************************************************************************** PP

                         TIGR01132  78 tGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkea...ladGivitpshnpp 151
                                       tGply+G+dthals+ a+ sv+evl+an+v+v+ q  + ytptp vs+ai++ n+ ++++   l+dGi+itpshnpp
  lcl|FitnessBrowser__SB2B:6937550  78 TGPLYLGMDTHALSQAAYLSVIEVLIANKVQVLAQRDDAYTPTPVVSQAIVAANRHQTGEdalLSDGIIITPSHNPP 154
                                       ***************************************************99986654422278************ PP

                         TIGR01132 152 edGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvvdlaairka 228
                                       +dGGikynpp+GGpae+++t +ie ran++l+++l gv+r+++  a   +++k++dl++pyv+ la+v+d+aai ka
  lcl|FitnessBrowser__SB2B:6937550 155 QDGGIKYNPPHGGPAEGDITSWIETRANHYLAHGLDGVRRVNYGIASGLSLLKHVDLISPYVQSLAEVIDMAAIAKA 231
                                       ***************************************************************************** PP

                         TIGR01132 229 glrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllklkdkydlafgnd 305
                                       g+r+GvdplGG+g++yw++iae+y+l++ +vn+a+d+tf fm ldkdGkirmdcsspyamagll  kd++d+ +gnd
  lcl|FitnessBrowser__SB2B:6937550 232 GVRMGVDPLGGSGIHYWQPIAEHYGLNIEVVNQAIDPTFDFMPLDKDGKIRMDCSSPYAMAGLLVHKDEFDICVGND 308
                                       ***************************************************************************** PP

                         TIGR01132 306 adadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgrklvevpvGfkwfvdGl 382
                                       +d+drhGiv p +Gl++pnhylavai+yl  hr++wa+++avGktlvssalid+v    g  l+evpvGfkwfvdGl
  lcl|FitnessBrowser__SB2B:6937550 309 PDYDRHGIVCPGSGLMDPNHYLAVAIDYLLGHRPNWAKTLAVGKTLVSSALIDKVCMAHGVPLMEVPVGFKWFVDGL 385
                                       ***************************************************************************** PP

                         TIGR01132 383 ldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaakyGdpiyaridaaatsaqk 459
                                        d+s+ fGGeesaGa+fl+ dG++w+tdkdG ilallaaei+avtGk+p +ry+el a++G  +y+rid++ +++ k
  lcl|FitnessBrowser__SB2B:6937550 386 ADSSVCFGGEESAGAAFLKMDGSTWCTDKDGFILALLAAEILAVTGKTPAERYEELVAEHGRSFYKRIDSPLNPKMK 462
                                       ***************************************************************************** PP

                         TIGR01132 460 arlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfkgeehlkeieke 536
                                       a++  l ++++ at++aGdaita ltkapGngaaiGG+kv td+gwfaarpsGte ++k+yaesf  e+hl e+ ++
  lcl|FitnessBrowser__SB2B:6937550 463 AKFGALNAQTLGATSVAGDAITAVLTKAPGNGAAIGGIKVCTDKGWFAARPSGTEPLFKLYAESFVSEAHLGELISD 539
                                       ***************************************************************************** PP

                         TIGR01132 537 aeeivdevl 545
                                       a+ ++  +l
  lcl|FitnessBrowser__SB2B:6937550 540 AQSLLGTAL 548
                                       **9987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (560 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: 8.25
//
[ok]

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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