GapMind for catabolism of small carbon sources

 

Alignments 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:

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:

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:

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:

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