Alignments for a candidate for pgmA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Klebsiella michiganensis M5al

Align phosphoglucomutase; EC 5.4.2.2 (characterized)
to candidate BWI76_RS08290 BWI76_RS08290 phosphoglucomutase, alpha-D-glucose phosphate-specific

Query= CharProtDB::CH_002452
         (546 letters)



>FitnessBrowser__Koxy:BWI76_RS08290
          Length = 546

 Score = 1049 bits (2713), Expect = 0.0
 Identities = 520/546 (95%), Positives = 534/546 (97%)

Query: 1   MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPH 60
           MAI  RAGQPAQQSDLINVAQLTAQYYVLKPE GNAEHAVKFGTSGHRGSAARH+FNE H
Sbjct: 1   MAIDKRAGQPAQQSDLINVAQLTAQYYVLKPEVGNAEHAVKFGTSGHRGSAARHNFNEQH 60

Query: 61  ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120
           ILAIAQAIAE+RAKNGI GPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT
Sbjct: 61  ILAIAQAIAEDRAKNGIAGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120

Query: 121 PAVSNAILVHNKKGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANAL 180
           PA+SNAILVHNKK GPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVE+RAN L
Sbjct: 121 PAISNAILVHNKKDGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVENRANEL 180

Query: 181 LADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGSG 240
           LA GL+GVKRISLD A+ASGHVKEQDLVQPF+EGLADIVDMAAIQKAGLTLGVDPLGGSG
Sbjct: 181 LAAGLQGVKRISLDAALASGHVKEQDLVQPFIEGLADIVDMAAIQKAGLTLGVDPLGGSG 240

Query: 241 IEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLA 300
           IEYWKRI E+YNLNLTIVND VDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLA
Sbjct: 241 IEYWKRIAEHYNLNLTIVNDHVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLA 300

Query: 301 FANDPDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRVVN 360
           FANDPDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRVVN
Sbjct: 301 FANDPDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRVVN 360

Query: 361 DLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAAE 420
           DLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAAE
Sbjct: 361 DLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAAE 420

Query: 421 ITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSASTLAGDPITA 480
           ITAVTGKNPQ+HY+ELA+RFGAPSYNRLQA+ATSAQKAALSKLSPEMVSASTLAGDPITA
Sbjct: 421 ITAVTGKNPQQHYDELAERFGAPSYNRLQASATSAQKAALSKLSPEMVSASTLAGDPITA 480

Query: 481 RLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEIVS 540
           RLTAAPGNGA+IGGLKVMTDNGWFAARPSGTEDAYKIYCESFLG EHR+QIEKEAVEIVS
Sbjct: 481 RLTAAPGNGAAIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGAEHRQQIEKEAVEIVS 540

Query: 541 EVLKNA 546
           EVLKNA
Sbjct: 541 EVLKNA 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: 1167
Number of extensions: 43
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: 546
Length adjustment: 35
Effective length of query: 511
Effective length of database: 511
Effective search space:   261121
Effective search space used:   261121
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 BWI76_RS08290 BWI76_RS08290 (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.31772.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
          0 1059.5   0.7          0 1059.3   0.7    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS08290  BWI76_RS08290 phosphoglucomutase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS08290  BWI76_RS08290 phosphoglucomutase, alpha-D-glucose phosphate-specific
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1059.3   0.7         0         0       1     546 []       1     544 [.       1     544 [. 1.00

  Alignments for each domain:
  == domain 1  score: 1059.3 bits;  conditional E-value: 0
                               TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvev 71 
                                             mai++raGq+aqq+dl++va+l+a+yy+lkp+ +na+++v+fGtsGhrGsa+++ fne+hilaiaqa++e 
  lcl|FitnessBrowser__Koxy:BWI76_RS08290   1 MAIDKRAGQPAQQSDLINVAQLTAQYYVLKPEVGNAEHAVKFGTSGHRGSAARHNFNEQHILAIAQAIAED 71 
                                             799******************************************************************** PP

                               TIGR01132  72 raaqGitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGi 142
                                             ra++Gi+Gp+y+Gkdthalsepaf+svlevlaan+v+vivqenn++tptpa+s+ail++nk k+++ladGi
  lcl|FitnessBrowser__Koxy:BWI76_RS08290  72 RAKNGIAGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPTPAISNAILVHNK-KDGPLADGI 141
                                             *************************************************************.********* PP

                               TIGR01132 143 vitpshnppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyv 213
                                             vitpshnppedGGikynppnGGpa+t+vtk++e+ranell+++l+gvkr++l+ al+s++vke+dlv+p++
  lcl|FitnessBrowser__Koxy:BWI76_RS08290 142 VITPSHNPPEDGGIKYNPPNGGPADTNVTKVVENRANELLAAGLQGVKRISLDAALASGHVKEQDLVQPFI 212
                                             *********************************************************************** PP

                               TIGR01132 214 ddladvvdlaairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcss 284
                                             ++lad+vd+aai+kagl+lGvdplGG+g++ywk+iae+ynl+lt+vn++vd+tfrfm+ldkdG+irmdcss
  lcl|FitnessBrowser__Koxy:BWI76_RS08290 213 EGLADIVDMAAIQKAGLTLGVDPLGGSGIEYWKRIAEHYNLNLTIVNDHVDQTFRFMHLDKDGAIRMDCSS 283
                                             *********************************************************************** PP

                               TIGR01132 285 pyamagllklkdkydlafgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssa 355
                                             ++amagll+l+dk+dlaf+nd+d+drhGivtp +Gl+npnhylavai+yl++hr+qw+++vavGktlvssa
  lcl|FitnessBrowser__Koxy:BWI76_RS08290 284 ECAMAGLLALRDKFDLAFANDPDYDRHGIVTP-AGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSA 353
                                             ********************************.************************************** PP

                               TIGR01132 356 lidrvvadlgrklvevpvGfkwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitav 426
                                             +idrvv+dlgrklvevpvGfkwfvdGl+dgs+GfGGeesaGasflr+dGt+wstdkdGii++llaaeitav
  lcl|FitnessBrowser__Koxy:BWI76_RS08290 354 MIDRVVNDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAAEITAV 424
                                             *********************************************************************** PP

                               TIGR01132 427 tGknpqqrydelaakyGdpiyaridaaatsaqkarlkklspdevsattlaGdaitakltkapGngaaiGGl 497
                                             tGknpqq+ydela+++G+p+y+r++a+atsaqka+l+klsp++vsa+tlaGd+ita+lt+apGngaaiGGl
  lcl|FitnessBrowser__Koxy:BWI76_RS08290 425 TGKNPQQHYDELAERFGAPSYNRLQASATSAQKAALSKLSPEMVSASTLAGDPITARLTAAPGNGAAIGGL 495
                                             *********************************************************************** PP

                               TIGR01132 498 kvttdegwfaarpsGtedvykiyaesfkgeehlkeiekeaeeivdevlk 546
                                             kv+td+gwfaarpsGted+ykiy+esf g+eh+++iekea eiv+evlk
  lcl|FitnessBrowser__Koxy:BWI76_RS08290 496 KVMTDNGWFAARPSGTEDAYKIYCESFLGAEHRQQIEKEAVEIVSEVLK 544
                                             ***********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (546 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: 00:00:00.03
# Mc/sec: 9.29
//
[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