GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24015 in Shewanella loihica PV-4

Align ABC transporter related (characterized, see rationale)
to candidate 5210736 Shew_3164 ABC transporter-related protein (RefSeq)

Query= uniprot:B2TBJ9
         (263 letters)



>FitnessBrowser__PV4:5210736
          Length = 241

 Score =  241 bits (615), Expect = 1e-68
 Identities = 123/247 (49%), Positives = 173/247 (70%), Gaps = 11/247 (4%)

Query: 9   LSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVSLA 68
           + + N+HK FGD+ VLKGI     +G+V+S++G SGSGKSTFLRC+NLLE P  G + + 
Sbjct: 2   IKISNLHKYFGDNQVLKGIDESIARGEVVSVIGPSGSGKSTFLRCINLLEQPTQGEIVID 61

Query: 69  GEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQKRSR 128
           G+ +            +    +D++R ++GMVFQNFNL+ H TV +N+   P+++   ++
Sbjct: 62  GQSIT-----------APDACIDKLRQKVGMVFQNFNLFPHKTVQQNITLAPVKLGLMTQ 110

Query: 129 AESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALDPE 188
           AE+  EA  LL +VGL++K   YPA LSGGQ+QRVAIARALAM P++MLFDEPTSALDPE
Sbjct: 111 AEADSEAMRLLDQVGLSDKASAYPASLSGGQKQRVAIARALAMKPELMLFDEPTSALDPE 170

Query: 189 LVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVECKSD 248
           +VG+VL VM+ LA+ G TM++VTHEMGFA+ VS+RV+F+  G V     P  +F + +  
Sbjct: 171 MVGDVLDVMKQLAQAGMTMVIVTHEMGFAKDVSDRVIFMDGGYVVESNVPALLFGQPQEP 230

Query: 249 RFRQFVS 255
           R + F+S
Sbjct: 231 RTQAFLS 237


Lambda     K      H
   0.318    0.133    0.377 

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: 178
Number of extensions: 5
Number of successful extensions: 2
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: 263
Length of database: 241
Length adjustment: 24
Effective length of query: 239
Effective length of database: 217
Effective search space:    51863
Effective search space used:    51863
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 (21.7 bits)
S2: 46 (22.3 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