Alignments for a candidate for pgmA in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Shewanella oneidensis MR-1

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate 201480 SO2336 phosphoglucomutase, alpha-D-glucose phosphate-specific (NCBI ptt file)

Query= BRENDA::A0A0H3NJ17
         (546 letters)



>FitnessBrowser__MR1:201480
          Length = 550

 Score =  645 bits (1665), Expect = 0.0
 Identities = 321/548 (58%), Positives = 405/548 (73%), Gaps = 5/548 (0%)

Query: 1   MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAGRHSFNEPH 60
           MAIH RAGQ A Q DL+N+ +L + YY +KP    AE  V FGTSGHRG+A + SFN+ H
Sbjct: 1   MAIHQRAGQIASQMDLVNIPKLMSHYYSIKPNMDAAEQRVTFGTSGHRGTAFQGSFNQDH 60

Query: 61  ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120
           I AI QA+ + R    I GP ++G DTHALS  A++S +EVLAAN V V +Q+N+GFTPT
Sbjct: 61  IWAITQAVVDYRQSVNIEGPLFLGIDTHALSYAAYVSAIEVLAANKVTVYIQQNDGFTPT 120

Query: 121 PAVSNAILVHN----KKGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDR 176
           P VS+AI+  N    + G  L+DG++ITPSHNPP+DGGIKYNPP+GGPA+ N+T  +E R
Sbjct: 121 PVVSHAIICANHAAAQNGALLSDGLIITPSHNPPQDGGIKYNPPHGGPAEGNITAWIESR 180

Query: 177 ANALLAGGLQGVKRISLDAAMASGHVKAVDLVQPFVEGLADIVDMAAIQKAGLTLGVDPL 236
           AN  L   L+GV +++   A+ASG+V A+DL+ P+V  L ++VDM AI KA L LGVDPL
Sbjct: 181 ANDYLRAALKGVNKLAYADALASGYVHAIDLITPYVADLENVVDMHAIAKANLKLGVDPL 240

Query: 237 GGSGIEYWKRIAEHYKLNLTLVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDK 296
           GGSGI YW  IA+HY +++TLVND+VD +F FM LDKDG IRMDCSS  AMAGLLA ++ 
Sbjct: 241 GGSGIHYWAPIAKHYGIDITLVNDKVDPSFSFMSLDKDGKIRMDCSSPYAMAGLLAHKES 300

Query: 297 FDLAFANDPDYDRHGIVTPA-GLMNPNHYLAVAINYLFQHRPLWGKDVAVGKTLVSSAMI 355
           FDL   NDPDYDRHGIV P  GLM+PNHYLAVAI+YL  HRP W   +A+GKTLVSSA+I
Sbjct: 301 FDLCVGNDPDYDRHGIVCPGTGLMDPNHYLAVAIDYLLTHRPEWSDSLAIGKTLVSSALI 360

Query: 356 DRVVNDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMC 415
           D++    G+KL+EVPVGFKWFVDGL + +  FGGEESAGA+FLR DGT W TDKDG I+ 
Sbjct: 361 DKICVFHGKKLLEVPVGFKWFVDGLAEATIAFGGEESAGAAFLRRDGTTWCTDKDGFILV 420

Query: 416 LLAAEITAVTGKNPQEHYNELAARFGAPSYNRLQASATSAQKAALSKLSPEMVSASTLAG 475
           LLAAE+ AVTGK P + + EL A+FG   Y R+ +  +   KA  +KL+ + ++A+ LAG
Sbjct: 421 LLAAEMLAVTGKTPGQRHQELVAQFGQSFYKRIDSPISLENKAKFAKLNADTLNATMLAG 480

Query: 476 DPITARLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEA 535
           + I A LT APGN ASIGG+KV T NGWFAARPSGTE  +KIY ESF+ E+H  +I K+A
Sbjct: 481 EKIEAVLTHAPGNNASIGGIKVTTTNGWFAARPSGTEALFKIYGESFISEQHLAEIIKDA 540

Query: 536 VEIVSEVL 543
             ++ + L
Sbjct: 541 QALIDKAL 548


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: 885
Number of extensions: 35
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: 550
Length adjustment: 36
Effective length of query: 510
Effective length of database: 514
Effective search space:   262140
Effective search space used:   262140
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 201480 SO2336 (phosphoglucomutase, alpha-D-glucose phosphate-specific (NCBI ptt file))
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.13372.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   4.2e-261  853.0   0.9   4.8e-261  852.8   0.9    1.0  1  lcl|FitnessBrowser__MR1:201480  SO2336 phosphoglucomutase, alpha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201480  SO2336 phosphoglucomutase, alpha-D-glucose phosphate-specific (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  852.8   0.9  4.8e-261  4.8e-261       1     545 [.       1     548 [.       1     549 [. 0.99

  Alignments for each domain:
  == domain 1  score: 852.8 bits;  conditional E-value: 4.8e-261
                       TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraaqGitG 79 
                                     mai++raGq a q dl++++kl+++yy++kp+ + a+q+v+fGtsGhrG+a +g+fn+ hi ai+qavv++r+   i G
  lcl|FitnessBrowser__MR1:201480   1 MAIHQRAGQIASQMDLVNIPKLMSHYYSIKPNMDAAEQRVTFGTSGHRGTAFQGSFNQDHIWAITQAVVDYRQSVNIEG 79 
                                     89***************************************************************************** PP

                       TIGR01132  80 plyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkea...ladGivitpshnppedGG 155
                                     pl++G dthals  a+vs++evlaan+v v +q+n+++tptp vshai+  n++  ++   l+dG++itpshnpp+dGG
  lcl|FitnessBrowser__MR1:201480  80 PLFLGIDTHALSYAAYVSAIEVLAANKVTVYIQQNDGFTPTPVVSHAIICANHAAAQNgalLSDGLIITPSHNPPQDGG 158
                                     **************************************************9986544322378**************** PP

                       TIGR01132 156 ikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvvdlaairkaglrlGv 234
                                     ikynpp+GGpae+++t +ie ran++l++ lkgv +l ++ al+s+ v++ dl++pyv+dl +vvd+ ai ka+l+lGv
  lcl|FitnessBrowser__MR1:201480 159 IKYNPPHGGPAEGNITAWIESRANDYLRAALKGVNKLAYADALASGYVHAIDLITPYVADLENVVDMHAIAKANLKLGV 237
                                     ******************************************************************************* PP

                       TIGR01132 235 dplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllklkdkydlafgndadadrhGi 313
                                     dplGG+g++yw +ia++y++d+tlvn++vd++f fm+ldkdGkirmdcsspyamagll+ k+ +dl +gnd+d+drhGi
  lcl|FitnessBrowser__MR1:201480 238 DPLGGSGIHYWAPIAKHYGIDITLVNDKVDPSFSFMSLDKDGKIRMDCSSPYAMAGLLAHKESFDLCVGNDPDYDRHGI 316
                                     ******************************************************************************* PP

                       TIGR01132 314 vtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgrklvevpvGfkwfvdGlldgslGfGGe 392
                                     v p +Gl++pnhylavai+yl +hr++w++++a+Gktlvssalid++    g+kl+evpvGfkwfvdGl ++++ fGGe
  lcl|FitnessBrowser__MR1:201480 317 VCPGTGLMDPNHYLAVAIDYLLTHRPEWSDSLAIGKTLVSSALIDKICVFHGKKLLEVPVGFKWFVDGLAEATIAFGGE 395
                                     ******************************************************************************* PP

                       TIGR01132 393 esaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaakyGdpiyaridaaatsaqkarlkklspdevs 471
                                     esaGa+flr+dGt+w+tdkdG il llaae++avtGk+p+qr++el a++G+ +y+rid++ + ++ka+++kl +d++ 
  lcl|FitnessBrowser__MR1:201480 396 ESAGAAFLRRDGTTWCTDKDGFILVLLAAEMLAVTGKTPGQRHQELVAQFGQSFYKRIDSPISLENKAKFAKLNADTLN 474
                                     ******************************************************************************* PP

                       TIGR01132 472 attlaGdaitakltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfkgeehlkeiekeaeeivdevl 545
                                     at laG+ i a lt+apGn+a+iGG+kvtt +gwfaarpsGte ++kiy esf  e+hl ei k+a++++d++l
  lcl|FitnessBrowser__MR1:201480 475 ATMLAGEKIEAVLTHAPGNNASIGGIKVTTTNGWFAARPSGTEALFKIYGESFISEQHLAEIIKDAQALIDKAL 548
                                     **********************************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (550 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: 12.08
//
[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)
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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