GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1695 in Azospirillum brasilense Sp245

Align ABC transporter permease (characterized, see rationale)
to candidate AZOBR_RS29670 AZOBR_RS29670 ABC transporter permease

Query= uniprot:A0A165KC95
         (309 letters)



>FitnessBrowser__azobra:AZOBR_RS29670
          Length = 290

 Score =  187 bits (475), Expect = 3e-52
 Identities = 102/296 (34%), Positives = 162/296 (54%), Gaps = 18/296 (6%)

Query: 5   LQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPGA 64
           LQ ++N +VLG  YAL+ +G T+++GI++++NF HGE+   GA  ++   GMM     G 
Sbjct: 5   LQHLLNAVVLGGTYALLGIGLTLIFGIMRVVNFTHGELYTFGAYMAYMLAGMM-----GL 59

Query: 65  PGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIWK 124
             ++ L +A ++   + A + F +     RPL+ +     ++  IG  I +Q    ++W 
Sbjct: 60  NFFMSLAMAAVLGMALGALIEFTL----LRPLKGADIDTTMLVMIGAGIAMQAGEQLVWG 115

Query: 125 PNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRATAENP 184
              K  P+  P+ P  +G   +   ++ +LGV  + L     L+N T LG AMRAT ++P
Sbjct: 116 GVAKSVPSPFPTEPVVLGSVSVGMNRLFVLGVALLLLGGFYLLINRTKLGVAMRATFQDP 175

Query: 185 RVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVFGGI 244
             A+LMGV   ++ + TF +G+ LAA AG +    +     TMG L  LKAF   + GG+
Sbjct: 176 DTAALMGVNRGLMYTLTFALGSGLAATAGALLGPIF-VVTPTMGDLVALKAFAIVILGGL 234

Query: 245 GNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL 300
           GN+ GA +GG +L L E  G+GY        L S Y D   F+++I +L +RP GL
Sbjct: 235 GNIPGATIGGFVLALAEEFGAGY--------LSSGYRDAMGFLLIIAVLIVRPQGL 282


Lambda     K      H
   0.327    0.142    0.419 

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: 214
Number of extensions: 12
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: 309
Length of database: 290
Length adjustment: 27
Effective length of query: 282
Effective length of database: 263
Effective search space:    74166
Effective search space used:    74166
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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