GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Shewanella amazonensis SB2B

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 6937828 Sama_1969 ABC transporter, ATP-binding protein (RefSeq)

Query= TCDB::Q8DQH7
         (236 letters)



>FitnessBrowser__SB2B:6937828
          Length = 301

 Score =  106 bits (264), Expect = 6e-28
 Identities = 65/214 (30%), Positives = 110/214 (51%), Gaps = 5/214 (2%)

Query: 1   MSVLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKI 60
           MS++   NL+  YG   A+ DVS +V  G  V+L+G NGAGKTT++  + G ++P  G +
Sbjct: 1   MSLIVTRNLTKRYGSKTALDDVSLQVEAGAPVALVGPNGAGKTTLMSLMCGYIQPDGGSL 60

Query: 61  EFLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVF 120
           E LG     +P  + + G +  +P+   + P  +V E L   A L+    ++     +  
Sbjct: 61  EILGH----VPGSRQLLGKVCALPQDALLDPNFSVGEQLSFFASLQGFSAKDARREAERV 116

Query: 121 SRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQ 180
                L++        LS G  + +A+ +AL+ TP+L+LLDEP+ GL P   + + ++I 
Sbjct: 117 LELVELKDAARHKPTALSHGMGKRVAIAQALIGTPQLVLLDEPTAGLDPANARAVRELIS 176

Query: 181 DIQKQGTTVLLIEQNANKALAISDRGYVLETGKI 214
              +Q TT L+   N  +   + D    L+ GK+
Sbjct: 177 HASEQ-TTFLISSHNLEELERLCDTVLYLDKGKL 209


Lambda     K      H
   0.315    0.134    0.358 

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: 147
Number of extensions: 6
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: 236
Length of database: 301
Length adjustment: 25
Effective length of query: 211
Effective length of database: 276
Effective search space:    58236
Effective search space used:    58236
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: 42 (22.0 bits)
S2: 47 (22.7 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