GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1695 in Dinoroseobacter shibae DFL-12

Align ABC transporter permease (characterized, see rationale)
to candidate 3609311 Dshi_2696 inner-membrane translocator (RefSeq)

Query= uniprot:A0A165KC95
         (309 letters)



>FitnessBrowser__Dino:3609311
          Length = 554

 Score =  130 bits (326), Expect = 9e-35
 Identities = 94/299 (31%), Positives = 151/299 (50%), Gaps = 14/299 (4%)

Query: 4   LLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPG 63
           + Q +  GL LGS+  L A+G  + +G++ +IN AHGE++MIGA T++    +++ + P 
Sbjct: 258 MAQNVWFGLSLGSVLLLAAIGLAITFGVMGVINMAHGELVMIGAYTTFFVQEIIRTSFPH 317

Query: 64  APGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIW 123
              W  LL+A  +A  VA  +   IE+   R L   P L  L+   G+S++LQ     I+
Sbjct: 318 LFDWS-LLIAAPLAFAVAGAVGVAIERGCVRFLYGRP-LETLLATWGISLILQQTVRSIF 375

Query: 124 KPNYKPY--PTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRATA 181
            PN +    P+ + S  FE+G   IT  ++ IL       A L++++  T +G  MRA  
Sbjct: 376 GPNNREVGNPSWM-SGAFEVGQMTITYNRLWILLFALAVFAVLLFVLKKTAIGLQMRAVT 434

Query: 182 ENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVF 241
           +N  +A+ MG++   V + TF +GA +A +AG+   S        +G    + +F   VF
Sbjct: 435 QNRAMAANMGIRTGWVDAMTFGLGAGIAGLAGVA-LSQIDNVSPNLGQSYIVDSFMVVVF 493

Query: 242 GGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL 300
           GG GN+ G +     LG+       Y G +   +L      +  FI+L I    RP GL
Sbjct: 494 GGAGNIWGTLAAAFSLGIANKFLEPYAGAVLAKIL------VLVFIILFI--QKRPRGL 544


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: 302
Number of extensions: 8
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: 554
Length adjustment: 31
Effective length of query: 278
Effective length of database: 523
Effective search space:   145394
Effective search space used:   145394
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: 50 (23.9 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