GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA2 in Sinorhizobium meliloti 1021

Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate SM_b21130 SM_b21130 sulfate ABC transporter ATP-binding protein

Query= uniprot:P70970
         (276 letters)



>FitnessBrowser__Smeli:SM_b21130
          Length = 367

 Score =  141 bits (355), Expect = 2e-38
 Identities = 88/218 (40%), Positives = 129/218 (59%), Gaps = 14/218 (6%)

Query: 9   ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDLK 68
           AL D++  I+ G  +A++G +GSGK+TLL+ + GL  PT+G I  G     A KK     
Sbjct: 17  ALEDVSLDIRSGELIALLGPSGSGKTTLLRLVAGLESPTEGTIFFGDE--DASKKTVQ-- 72

Query: 69  KLRKKVGIVFQFPEHQLFEE-TVLKDISFG----PMNFGVKKEDAEQKAREMLQLVGLSE 123
             ++ +G VFQ   + LF   TVL +++FG    P        D  ++A ++L+LV LS 
Sbjct: 73  --QRNIGFVFQ--HYALFRHMTVLDNVAFGLKVRPAKRRPSAADIRRRAVDLLELVQLSG 128

Query: 124 ELLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGN 183
            L  R P +LSGGQ +RVA+A  +A++P VL+LDEP   LD + RKE+     E+H R  
Sbjct: 129 -LERRYPAQLSGGQRQRVALARAMAVEPNVLLLDEPFGALDAQVRKELRRWLREIHDRTG 187

Query: 184 LTTILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLF 221
            TTI VTH  E+A   AD ++VM KG I+  G+P +++
Sbjct: 188 HTTIFVTHDQEEALELADRVVVMSKGAIEQVGTPDEIY 225


Lambda     K      H
   0.318    0.136    0.380 

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: 247
Number of extensions: 14
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: 276
Length of database: 367
Length adjustment: 27
Effective length of query: 249
Effective length of database: 340
Effective search space:    84660
Effective search space used:    84660
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: 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