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

GapMind for catabolism of small carbon sources

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

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate 5210100 Shew_2544 phosphoglucomutase/phosphomannomutase alpha/beta/subunit (RefSeq)

Query= BRENDA::C6L2F4
         (596 letters)



>FitnessBrowser__PV4:5210100
          Length = 584

 Score =  327 bits (839), Expect = 6e-94
 Identities = 217/595 (36%), Positives = 322/595 (54%), Gaps = 47/595 (7%)

Query: 13  LEAAVNFWRSVDRREETQKETLELLKNLTEDELAKLFLARLEFGTAGLRGRMGAGFSRMN 72
           ++A +  W S+D   +++ E   L+    ++EL   F  RL FGTAG+RG +GAG  RMN
Sbjct: 5   IQARIKHWLSLDSDAKSRAEIQALVDQGAQEELVARFAGRLTFGTAGIRGVVGAGPMRMN 64

Query: 73  DVTIQQTTQGYCAFLVDVFGEDGKDRGVVIGFDARHNSRRFAQLTAAVFLSKGFRVQLFS 132
            + +QQT++G   +L     E+   RGVVIG+D RH+S++FA+  A+V  + GF+V L S
Sbjct: 65  RLVVQQTSKGVAEYLKAQV-ENAVSRGVVIGYDGRHDSKQFAEDAASVLTAAGFKVFLTS 123

Query: 133 DIVHTPMVPYTVVAANCIAGIMITASHNPKADNGYKVYAANGAQIIPPMDSEISAFINSN 192
            +  TP+V + V+     AGI++TASHNP   NGYKVY  NGAQIIPP D+ I+A I   
Sbjct: 124 KVAPTPLVAFGVLHLGAAAGIVVTASHNPPQYNGYKVYWGNGAQIIPPHDTGIAARI--E 181

Query: 193 LDFWSDVDEYFDSKTGMLTEKAANSSLLEDPLNTYVDAYIKDIA-ADLCVAEQQGSDLKF 251
           L   S VD     +T + T K     +LE+    Y  AY + +  A++  +  +   +  
Sbjct: 182 LAANSPVD-MLPLETAVETGKLV---MLEE---DYYQAYRQGVLNAEVLQSPARPELVSL 234

Query: 252 MYTAMHGVGTPMVKKMLAAFGFNDNLLTVDAQCTPDPEFPTVAFPNPEEKGALDLAFQEA 311
            YTAMHGVG  M + +L   G    + +V AQ  PD +FPTV FPNPEE GA+ L   EA
Sbjct: 235 AYTAMHGVGAEMAETLLKDIGVT-QVYSVAAQREPDGDFPTVNFPNPEEAGAMVLVMAEA 293

Query: 312 DSHGLTLVIANDPDADRFAAA--------EKCDGRWYQ-FTGDELGAILGAYAIKLREGQ 362
             HG  L  ANDPDADRFA A        E      YQ  TGD++G +LG Y +      
Sbjct: 294 HKHGAMLACANDPDADRFAVAVRKPAATPEMLASEAYQMLTGDQVGVLLGHYLL-----S 348

Query: 363 GISKSKMALICSAVSSRMLQKIAKENGCTFAETMTGFKWMENKAIEMEAEGLIPVFVYEE 422
             S  +  L C+ VSS +L +I++  G     T+TGFKW+ N  +  + +    +F YEE
Sbjct: 349 HASDDQRLLCCTIVSSSLLTRISEACGARCETTLTGFKWLTNVGMSKQTQENRFLFAYEE 408

Query: 423 ALGYALSQRVRDKDGVSAAAVWMQMAIDLYSRGQTVMDFLMSLRKRYGYFVTRN-SYFIC 481
           ALGY +   V DKDG+SA   ++Q+  +L ++G+T+ D L ++ ++YGY++ R  S  + 
Sbjct: 409 ALGYTVGSMVWDKDGLSALVAFVQLTAELAAKGETLWDRLETIYRQYGYYLNRQVSIALS 468

Query: 482 PDP------RLIQGLFKDFANGGNYPKQLGPFTIRRIRDVGRGY----DSEEQCSFPSNC 531
            +P        ++ L          P ++    +  + D+  G     D  E+       
Sbjct: 469 GEPGAPTIGEQLRAL---------DPSEIAGRALVSVDDISLGVRRFADGREETIDLPRS 519

Query: 532 EMLTVYLDNGAVVTLRGSGTEPKLK-YYAETSSTDPEQGLAELAKVIAAVISDFV 585
           ++L   L   A V +R SGTEPK+K YY        ++GLA++ +   A +++FV
Sbjct: 520 DVLIYRLQGNARVIVRPSGTEPKVKCYYEVVEPFGEQEGLADVQRRAEAAMAEFV 574


Lambda     K      H
   0.320    0.135    0.398 

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: 767
Number of extensions: 34
Number of successful extensions: 8
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: 596
Length of database: 584
Length adjustment: 37
Effective length of query: 559
Effective length of database: 547
Effective search space:   305773
Effective search space used:   305773
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

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, or view the source code.

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