GapMind for catabolism of small carbon sources

 

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

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 202699 SO3602 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)

Query= TCDB::Q8DQH8
         (254 letters)



>FitnessBrowser__MR1:202699
          Length = 376

 Score =  130 bits (326), Expect = 5e-35
 Identities = 82/253 (32%), Positives = 138/253 (54%), Gaps = 22/253 (8%)

Query: 4   LEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTLD 63
           + +  ++K FG   A+  + L++ EGE++GL+GP+G+GKTTL  ++ G+    EG  +  
Sbjct: 3   IRLTNISKKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGL----EGADS-- 56

Query: 64  GHLLNGK---SPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPA 120
           GH+  G    +   +    +G  FQN  LF+ +TV DNV  AFG      V     R   
Sbjct: 57  GHIHFGNRDVTQVHVRDRRVGFVFQNYALFRHMTVADNV--AFG----LEVIPKKQR--- 107

Query: 121 FYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAA 180
              S  E++ +   LL++  L   A+   + LS GQ++R+ + RALAT+P++L LDEP  
Sbjct: 108 --PSAAEIQKRVSHLLEMVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFG 165

Query: 181 GMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEI- 239
            ++ +   EL   +R + DE K T + + HD +  +E+++R+ V+  G +    TP E+ 
Sbjct: 166 ALDAKVRKELRRWLRSLHDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELY 225

Query: 240 -KTNKRVIEAYLG 251
            + N R +  +LG
Sbjct: 226 AQPNSRFVFDFLG 238


Lambda     K      H
   0.319    0.139    0.385 

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: 189
Number of extensions: 7
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: 254
Length of database: 376
Length adjustment: 27
Effective length of query: 227
Effective length of database: 349
Effective search space:    79223
Effective search space used:    79223
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: 48 (23.1 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