GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Shewanella amazonensis SB2B

Align High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)

Query= TCDB::P21630
         (233 letters)



>FitnessBrowser__SB2B:6936480
          Length = 341

 Score =  102 bits (254), Expect = 9e-27
 Identities = 73/228 (32%), Positives = 117/228 (51%), Gaps = 9/228 (3%)

Query: 2   LSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRYE 61
           LS   + + Y   Q L  +++ + +GEI  L+G +G GK+TLL T+ G    ++GSI   
Sbjct: 4   LSIQGLHSDYRGEQVLRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISAGSIAIN 63

Query: 62  GEELVGLPSSTIM--RKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMDKVLEL 119
           G + V      +   ++SI ++ +   +F  LTV +N+  G    DK    V+++++L L
Sbjct: 64  G-KTVSADGCFVAPEKRSIGMIFQDYALFPHLTVADNILFGVRQLDKQSRSVRLEEMLSL 122

Query: 120 --FPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGL-APIIIQQIFEII 176
                L +RY      +SGG+QQ ++I RAL  +P LLLLDEP   + A +    + EI 
Sbjct: 123 VKLEGLGKRYPHE---LSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALMLEIR 179

Query: 177 EQLRREGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNP 224
             L+   V+   V  + ++A   AD   + E GRIV H     L  +P
Sbjct: 180 AILKARNVSAVFVTHSKDEAFAFADTLALFEAGRIVQHGIPETLYQSP 227


Lambda     K      H
   0.318    0.136    0.374 

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: 165
Number of extensions: 10
Number of successful extensions: 4
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: 233
Length of database: 341
Length adjustment: 26
Effective length of query: 207
Effective length of database: 315
Effective search space:    65205
Effective search space used:    65205
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 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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