Alignments for a candidate for pgmA in Photobacterium jeanii R-40508

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Photobacterium jeanii R-40508

Align phosphoglucomutase; EC 5.4.2.2 (characterized)
to candidate WP_068329294.1 A3K86_RS06355 alpha-D-glucose phosphate-specific phosphoglucomutase

Query= CharProtDB::CH_002452
         (546 letters)



>NCBI__GCF_001650345.1:WP_068329294.1
          Length = 548

 Score =  787 bits (2032), Expect = 0.0
 Identities = 378/546 (69%), Positives = 449/546 (82%)

Query: 1   MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPH 60
           MAIH RAGQ AQQ D+ N+  L A Y++++P+A N +  V FGTSGHRG+A + +FN+ H
Sbjct: 1   MAIHPRAGQQAQQEDMHNIPALVANYFIIEPKADNLQQRVAFGTSGHRGTADKGTFNQHH 60

Query: 61  ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120
           I AIAQA+AE RA NG+TGP ++GKDTHALSEPAF S LEVL ANGV V++QE  G+TPT
Sbjct: 61  IWAIAQAVAEVRAANGVTGPLFLGKDTHALSEPAFTSTLEVLVANGVQVVIQEGKGYTPT 120

Query: 121 PAVSNAILVHNKKGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANAL 180
           P +S+AIL +NK     ADGIVITPSHNPP+DGGIKYNP +GGPA+  +T  +E RAN +
Sbjct: 121 PGISHAILCYNKANAEKADGIVITPSHNPPQDGGIKYNPVHGGPAEGELTTAIETRANEI 180

Query: 181 LADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGSG 240
           +A+GL  VKR+++++A AS  V E+DLV P+V+ L +++DMAAIQKA L +GVDPLGGSG
Sbjct: 181 IANGLVDVKRVAIEDAFASELVVEKDLVAPYVDDLVNVIDMAAIQKANLAIGVDPLGGSG 240

Query: 241 IEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLA 300
           IEYW++I  +Y LNLT+VN+ +D +FRFM LDKDG +RMDCSS  AMAGLLA +DK+DLA
Sbjct: 241 IEYWRQIANHYGLNLTLVNESIDPSFRFMSLDKDGVVRMDCSSPYAMAGLLAHKDKYDLA 300

Query: 301 FANDPDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRVVN 360
           F NDPDYDRHGIVTPAGLMNPNH+LAV I+YL++HRP W  DVAVGKTLVSSA+IDRVV 
Sbjct: 301 FGNDPDYDRHGIVTPAGLMNPNHFLAVCIDYLYRHRPDWSADVAVGKTLVSSALIDRVVA 360

Query: 361 DLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAAE 420
           DLGR+L EVPVGFKWFVDGL+ G  GFGGEESAGASFLR DGTPW+TDKDGI++CLLAAE
Sbjct: 361 DLGRELCEVPVGFKWFVDGLYSGRLGFGGEESAGASFLRTDGTPWATDKDGILLCLLAAE 420

Query: 421 ITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSASTLAGDPITA 480
           ITAVTGKNP ++Y EL ++ G   YNRLQA A   QKA LSKLSPEMV+A  LAGDPITA
Sbjct: 421 ITAVTGKNPHQYYLELVEKHGESKYNRLQAVANGEQKAVLSKLSPEMVAAEMLAGDPITA 480

Query: 481 RLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEIVS 540
           RLT A GNGA+IGGLKV TDNGWFAARPSGTED YKIYCESF GEEH + IE EA EIVS
Sbjct: 481 RLTHASGNGAAIGGLKVTTDNGWFAARPSGTEDIYKIYCESFKGEEHLRMIETEAQEIVS 540

Query: 541 EVLKNA 546
           +V  +A
Sbjct: 541 KVFADA 546


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: 983
Number of extensions: 32
Number of successful extensions: 1
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: 548
Length adjustment: 36
Effective length of query: 510
Effective length of database: 512
Effective search space:   261120
Effective search space used:   261120
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: 52 (24.6 bits)

Align candidate WP_068329294.1 A3K86_RS06355 (alpha-D-glucose phosphate-specific phosphoglucomutase)
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.3779398.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-306 1003.0   0.4   1.6e-306 1002.9   0.4    1.0  1  NCBI__GCF_001650345.1:WP_068329294.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001650345.1:WP_068329294.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1002.9   0.4  1.6e-306  1.6e-306       1     545 [.       1     543 [.       1     544 [. 1.00

  Alignments for each domain:
  == domain 1  score: 1002.9 bits;  conditional E-value: 1.6e-306
                             TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevra 73 
                                           mai+praGq+aqqed++++++lva+y+ ++p+a+n++q+v+fGtsGhrG+a+kgtfn++hi aiaqav+evra
  NCBI__GCF_001650345.1:WP_068329294.1   1 MAIHPRAGQQAQQEDMHNIPALVANYFIIEPKADNLQQRVAFGTSGHRGTADKGTFNQHHIWAIAQAVAEVRA 73 
                                           89*********************************************************************** PP

                             TIGR01132  74 aqGitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGivitp 146
                                           a+G+tGpl++Gkdthalsepaf+s+levl+an+v+v++qe ++ytptp++shail ynk  ++++adGivitp
  NCBI__GCF_001650345.1:WP_068329294.1  74 ANGVTGPLFLGKDTHALSEPAFTSTLEVLVANGVQVVIQEGKGYTPTPGISHAILCYNK-ANAEKADGIVITP 145
                                           ***********************************************************.8899********* PP

                             TIGR01132 147 shnppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladv 219
                                           shnpp+dGGikynp +GGpae+e+t+aie rane+++++l  vkr+ +e a +se+v ekdlv pyvddl++v
  NCBI__GCF_001650345.1:WP_068329294.1 146 SHNPPQDGGIKYNPVHGGPAEGELTTAIETRANEIIANGLVDVKRVAIEDAFASELVVEKDLVAPYVDDLVNV 218
                                           ************************************************************************* PP

                             TIGR01132 220 vdlaairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagll 292
                                           +d+aai+ka+l +GvdplGG+g++yw++ia++y+l+ltlvne++d++frfm+ldkdG++rmdcsspyamagll
  NCBI__GCF_001650345.1:WP_068329294.1 219 IDMAAIQKANLAIGVDPLGGSGIEYWRQIANHYGLNLTLVNESIDPSFRFMSLDKDGVVRMDCSSPYAMAGLL 291
                                           ************************************************************************* PP

                             TIGR01132 293 klkdkydlafgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlg 365
                                           + kdkydlafgnd+d+drhGivtp +Gl+npnh+lav+i+yly+hr++w+a+vavGktlvssalidrvvadlg
  NCBI__GCF_001650345.1:WP_068329294.1 292 AHKDKYDLAFGNDPDYDRHGIVTP-AGLMNPNHFLAVCIDYLYRHRPDWSADVAVGKTLVSSALIDRVVADLG 363
                                           ************************.************************************************ PP

                             TIGR01132 366 rklvevpvGfkwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydel 438
                                           r+l+evpvGfkwfvdGl++g+lGfGGeesaGasflr+dGt+w+tdkdGi+l+llaaeitavtGknp+q+y el
  NCBI__GCF_001650345.1:WP_068329294.1 364 RELCEVPVGFKWFVDGLYSGRLGFGGEESAGASFLRTDGTPWATDKDGILLCLLAAEITAVTGKNPHQYYLEL 436
                                           ************************************************************************* PP

                             TIGR01132 439 aakyGdpiyaridaaatsaqkarlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarps 511
                                            +k+G+  y+r++a+a+++qka+l+klsp++v+a+ laGd+ita+lt+a GngaaiGGlkvttd+gwfaarps
  NCBI__GCF_001650345.1:WP_068329294.1 437 VEKHGESKYNRLQAVANGEQKAVLSKLSPEMVAAEMLAGDPITARLTHASGNGAAIGGLKVTTDNGWFAARPS 509
                                           ************************************************************************* PP

                             TIGR01132 512 Gtedvykiyaesfkgeehlkeiekeaeeivdevl 545
                                           Gted+ykiy+esfkgeehl+ ie+ea+eiv++v+
  NCBI__GCF_001650345.1:WP_068329294.1 510 GTEDIYKIYCESFKGEEHLRMIETEAQEIVSKVF 543
                                           *******************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (548 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 20.09
//
[ok]

This GapMind analysis is from Sep 24 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