Alignments for a candidate for pgmA in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Shewanella loihica PV-4

Align phosphoglucomutase; EC 5.4.2.2 (characterized)
to candidate 5209451 Shew_1922 phosphoglucomutase (RefSeq)

Query= CharProtDB::CH_002452
         (546 letters)



>FitnessBrowser__PV4:5209451
          Length = 559

 Score =  636 bits (1641), Expect = 0.0
 Identities = 317/558 (56%), Positives = 400/558 (71%), Gaps = 15/558 (2%)

Query: 1   MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPH 60
           MA+H RAG+PAQQ DL+N+ +L + YY L P+  N    V FGTSGHRG A   SFNE H
Sbjct: 1   MALHERAGKPAQQRDLVNIPKLMSHYYRLSPDVTNDAQKVTFGTSGHRGCAFNKSFNEKH 60

Query: 61  ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120
           ILAI QA+ + R + GI GP  VG DTHALS+ A+++ LEVL ANGV VIV +N+ +TPT
Sbjct: 61  ILAIVQAVVDHRIEAGIKGPMIVGIDTHALSQAAYVTALEVLTANGVQVIVAKNDEYTPT 120

Query: 121 PAVSNAILVHNKKGGP---------LADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTK 171
           P VS+AI+  N+  G          L DG++ITPSHNPP+DGGIKYNPP+GGPA+  +T 
Sbjct: 121 PVVSHAIIAANRVQGAGLTYGLNYGLTDGLIITPSHNPPQDGGIKYNPPHGGPAEGGITA 180

Query: 172 VVEDRANALLADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTL 231
            VE RAN  LA  L+GVKR++   A+ +  ++E+DL+  +VE L  ++DM AI++AG+ +
Sbjct: 181 WVEQRANEYLAKQLEGVKRLTYSVAVTTSLIQERDLMAAYVEDLEQVIDMQAIKQAGIRI 240

Query: 232 GVDPLGGSGIEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLL 291
           GVDPLGGSGI YW +I E Y L++T+VND++D  F FM LDKDG IRMDCSS  AMAGLL
Sbjct: 241 GVDPLGGSGIHYWAKIAERYGLDITLVNDRIDPAFGFMPLDKDGKIRMDCSSPYAMAGLL 300

Query: 292 ALRDKFDLAFANDPDYDRHGIVTP-AGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLV 350
             +D FD+ F NDPDYDRHGIV P +GLMNPNHYLAVAI YL  HRPQW  D+ +GKTLV
Sbjct: 301 VHQDAFDICFGNDPDYDRHGIVCPGSGLMNPNHYLAVAIEYLLSHRPQWSADLKIGKTLV 360

Query: 351 SSAMIDRVVNDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKD 410
           SSAMID+V  +  R L EVPVGFKWFV+GL D SF FGGEESAGA+FLR DG  W TDKD
Sbjct: 361 SSAMIDKVCREQSRSLCEVPVGFKWFVEGLADASFAFGGEESAGAAFLRRDGGSWCTDKD 420

Query: 411 GIIMCLLAAEITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSA 470
           G I+ LLAAEI AVTGK P + Y E+ +R G   Y R+ +     +KA  ++L  E ++ 
Sbjct: 421 GFILALLAAEILAVTGKTPAKLYAEMVERHGESFYKRIDSPVNPKRKAKFNQLVSEPLNV 480

Query: 471 STL-----AGDPITARLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGE 525
           S L     AGD I   LT APGNGA+IGG+KV+T+  WFAARPSGTE  +K+Y ESF+ E
Sbjct: 481 SDLGCEAMAGDAILEVLTHAPGNGAAIGGIKVVTEKAWFAARPSGTEALFKLYGESFVSE 540

Query: 526 EHRKQIEKEAVEIVSEVL 543
            H +Q+ ++A +++  +L
Sbjct: 541 AHLEQVLEQAQQMIERLL 558


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: 925
Number of extensions: 36
Number of successful extensions: 5
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: 559
Length adjustment: 36
Effective length of query: 510
Effective length of database: 523
Effective search space:   266730
Effective search space used:   266730
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 5209451 Shew_1922 (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.29345.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   6.7e-259  845.7   0.0   7.5e-259  845.5   0.0    1.0  1  lcl|FitnessBrowser__PV4:5209451  Shew_1922 phosphoglucomutase (Re


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209451  Shew_1922 phosphoglucomutase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  845.5   0.0  7.5e-259  7.5e-259       1     545 [.       1     558 [.       1     559 [] 0.96

  Alignments for each domain:
  == domain 1  score: 845.5 bits;  conditional E-value: 7.5e-259
                        TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraaqGit 78 
                                      ma+++raG++aqq dl++++kl+++yy+l pd  n aqkv+fGtsGhrG+a +++fne+hilai qavv++r + Gi 
  lcl|FitnessBrowser__PV4:5209451   1 MALHERAGKPAQQRDLVNIPKLMSHYYRLSPDVTNDAQKVTFGTSGHRGCAFNKSFNEKHILAIVQAVVDHRIEAGIK 78 
                                      799*************************************************************************** PP

                        TIGR01132  79 GplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkke........aladGivitpsh 148
                                      Gp+ +G dthals+ a+v++levl+an+v+viv +n+ ytptp vshai++ n+ + +        +l+dG++itpsh
  lcl|FitnessBrowser__PV4:5209451  79 GPMIVGIDTHALSQAAYVTALEVLTANGVQVIVAKNDEYTPTPVVSHAIIAANRVQGAgltyglnyGLTDGLIITPSH 156
                                      *****************************************************9766511122222578********* PP

                        TIGR01132 149 nppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvvdlaair 226
                                      npp+dGGikynpp+GGpae+ +t ++e+rane+l+++l+gvkrl+++ a+ +++++e+dl+  yv+dl +v+d++ai+
  lcl|FitnessBrowser__PV4:5209451 157 NPPQDGGIKYNPPHGGPAEGGITAWVEQRANEYLAKQLEGVKRLTYSVAVTTSLIQERDLMAAYVEDLEQVIDMQAIK 234
                                      ****************************************************************************** PP

                        TIGR01132 227 kaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllklkdkydlafgn 304
                                      +ag+r+GvdplGG+g++yw +iae+y+ld+tlvn+ +d++f fm ldkdGkirmdcsspyamagll  +d +d+ fgn
  lcl|FitnessBrowser__PV4:5209451 235 QAGIRIGVDPLGGSGIHYWAKIAERYGLDITLVNDRIDPAFGFMPLDKDGKIRMDCSSPYAMAGLLVHQDAFDICFGN 312
                                      ****************************************************************************** PP

                        TIGR01132 305 dadadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgrklvevpvGfkwfvdGl 382
                                      d+d+drhGiv p +Gl+npnhylavaieyl +hr+qw+a++ +Gktlvssa+id+v  + +r l+evpvGfkwfv+Gl
  lcl|FitnessBrowser__PV4:5209451 313 DPDYDRHGIVCPGSGLMNPNHYLAVAIEYLLSHRPQWSADLKIGKTLVSSAMIDKVCREQSRSLCEVPVGFKWFVEGL 390
                                      ****************************************************************************** PP

                        TIGR01132 383 ldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaakyGdpiyaridaaatsaqka 460
                                       d+s+ fGGeesaGa+flr+dG  w+tdkdG ilallaaei+avtGk+p + y e+ +++G+ +y+rid++ ++++ka
  lcl|FitnessBrowser__PV4:5209451 391 ADASFAFGGEESAGAAFLRRDGGSWCTDKDGFILALLAAEILAVTGKTPAKLYAEMVERHGESFYKRIDSPVNPKRKA 468
                                      ****************************************************************************** PP

                        TIGR01132 461 rlkklspdevs.....attlaGdaitakltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfkgeehlkei 533
                                      ++++l ++ +       + +aGdai   lt+apGngaaiGG+kv+t+++wfaarpsGte ++k+y esf  e+hl+++
  lcl|FitnessBrowser__PV4:5209451 469 KFNQLVSEPLNvsdlgCEAMAGDAILEVLTHAPGNGAAIGGIKVVTEKAWFAARPSGTEALFKLYGESFVSEAHLEQV 546
                                      ****9887544002225678********************************************************** PP

                        TIGR01132 534 ekeaeeivdevl 545
                                       ++a++++++ l
  lcl|FitnessBrowser__PV4:5209451 547 LEQAQQMIERLL 558
                                      *******99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (559 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 0.02s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 7.56
//
[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