GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Shewanella amazonensis SB2B

Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate 6938122 Sama_2243 phosphoglucosamine mutase (RefSeq)

Query= SwissProt::Q68BJ6
         (456 letters)



>FitnessBrowser__SB2B:6938122
          Length = 452

 Score =  218 bits (555), Expect = 3e-61
 Identities = 160/456 (35%), Positives = 233/456 (51%), Gaps = 31/456 (6%)

Query: 3   KLFGTFGVRGIANE-EITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDAL 61
           K FGT GVRG   E  ITP+FA+K+G A GT++   G +   V++G+DTR+SG ML+ A+
Sbjct: 4   KYFGTDGVRGKVGEFPITPDFAMKLGWAAGTVMAASGTKE--VIIGKDTRLSGYMLESAM 61

Query: 62  ISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121
            +G  + G +V   G  PTPAI + T+ F AD G VI+ASHNP   NGIK     G  L 
Sbjct: 62  EAGFCAAGVNVALTGPLPTPAIAYLTSTFRADAGVVISASHNPYYDNGIKFFSNTGTKLT 121

Query: 122 KEREAIVEELFFSEDFHRAKW----NEIGELRK-EDIIKPYIEAIK----NRVDVEAIKK 172
            E+E  +E L  S     A      +++G++R+  D    YIE  K    N + +  +K 
Sbjct: 122 DEQELEIERLLVSAIEGGAMTCVASDKLGKVRRINDAAGRYIEFCKGTFPNSLSLTGLK- 180

Query: 173 RRPFVVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVK 232
               +VVD+++GA       + RELG +V+S+N  PDG     N      ++      V 
Sbjct: 181 ----IVVDSAHGAAYHIAKNVYRELGAEVISINDKPDG--ININEHCGATHMDSLQTAVM 234

Query: 233 ALGADFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLR--ENGGGLLVTTIATSNL 290
              AD G+A DGDADR + +D  G+ I GD    L+A +  +  E   G++ T +  SNL
Sbjct: 235 IHEADLGIALDGDADRLMMVDSKGQVIDGDALLYLLAKSAQQRGEQVSGVIGTLM--SNL 292

Query: 291 LDDIAKRN-GAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKI 349
             + A  N G    R KVGD  V   L E    +GGE +G ++  DF    D  + + ++
Sbjct: 293 GFEQALANLGIPFKRAKVGDRYVVELLKETGWRLGGENSGHLLMLDFTTTGDAIVASLQV 352

Query: 350 VEIFAKSGKKFSELIDELPKYYQFKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKI 409
           +    +SG   ++ I EL  + Q      + G+     A V          + T +    
Sbjct: 353 LRALLESGAGLADAITELNMFPQVLINVRLNGN-----AAVGLSHPSVSDAVATAESA-- 405

Query: 410 IFDDGWVLVRASGTEPIIRIFSEAKSEEKAREYLEL 445
           + +DG VL+R SGTEP+IR+  EAK   KA +Y EL
Sbjct: 406 LGNDGRVLLRKSGTEPLIRVMVEAKDAVKANQYAEL 441


Lambda     K      H
   0.317    0.139    0.396 

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: 494
Number of extensions: 30
Number of successful extensions: 7
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: 456
Length of database: 452
Length adjustment: 33
Effective length of query: 423
Effective length of database: 419
Effective search space:   177237
Effective search space used:   177237
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: 51 (24.3 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