GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1694 in Dinoroseobacter shibae DFL-12

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 3608584 Dshi_1978 inner-membrane translocator (RefSeq)

Query= uniprot:A0A165KER0
         (358 letters)



>FitnessBrowser__Dino:3608584
          Length = 317

 Score =  113 bits (283), Expect = 6e-30
 Identities = 96/321 (29%), Positives = 150/321 (46%), Gaps = 29/321 (9%)

Query: 30  VRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFALMASPHLADNFAAFAAM 89
           V  A +A +  +  LGLN+  G  GL + G VAF+  G Y   ++     A +   F   
Sbjct: 9   VFFATIASILAIAVLGLNLHWGNTGLFNGGVVAFFGAGGYATLILGGTPQAAHLGGFG-- 66

Query: 90  FPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIVTLGFGEIIRIFLNNLDHP 149
            P GL     +VI  A LLA   G +    T++LR DYLAI T G   +   F N + + 
Sbjct: 67  LPYGLALLGGLVI--AGLLAWLVGLL----TIRLRHDYLAIATFG---VAVAFENLVRNA 117

Query: 150 VNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYYYLFLVLVVVSVIICY---- 205
             L  G  GL   +      +  G               Y   F   V+ ++I  Y    
Sbjct: 118 QRLAGGASGLRGFERPLADTIPPG-------------LAYNAAFFAFVLAALIATYLGLE 164

Query: 206 RLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVSGAMFGAFQGFVSPE 265
           RL     GR   AIREDE AA+A+G +   ++L AF +G+   G++GA++  F  F+SP+
Sbjct: 165 RLIRGPFGRLLRAIREDETAARALGKSPDRIRLTAFVIGSVILGLAGALYATFYAFISPQ 224

Query: 266 SFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPLQAMTDGRLDSAILR 325
               + +  I AM+++GG G+  G I GA L+        +      A  + +L +  ++
Sbjct: 225 DVLPILTFQIWAMLIVGGAGNNRGAIAGAFLIWGAWTASGWALSRF-APIEVQLYTGSIQ 283

Query: 326 QLLIALAMIIIMLLRPRGLWP 346
            +LI   ++ ++L RP+GL+P
Sbjct: 284 FVLIGCVIVGMLLWRPQGLFP 304


Lambda     K      H
   0.328    0.144    0.430 

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: 309
Number of extensions: 19
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: 358
Length of database: 317
Length adjustment: 28
Effective length of query: 330
Effective length of database: 289
Effective search space:    95370
Effective search space used:    95370
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: 49 (23.5 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