GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA2 in Rhodobacter viridis JA737

Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate WP_110805339.1 C8J30_RS08100 ABC transporter ATP-binding protein

Query= uniprot:P70970
         (276 letters)



>NCBI__GCF_003217355.1:WP_110805339.1
          Length = 348

 Score =  142 bits (359), Expect = 8e-39
 Identities = 79/211 (37%), Positives = 130/211 (61%), Gaps = 10/211 (4%)

Query: 12  DINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDLKKLR 71
           D N ++++G +++++G +G GK+T+L+ + G   PT G I++      AGK+  DLK  +
Sbjct: 21  DFNLTVEKGEFISLLGPSGCGKTTVLRMVAGFELPTSGAITI------AGKEVTDLKPNQ 74

Query: 72  KKVGIVFQFPEHQLFEE-TVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLSEELLDRSP 130
           + +G+VFQ   + LF   TV +++ FG    G  K   +++  EML L+GL + L +R P
Sbjct: 75  RNIGMVFQ--AYALFPNLTVAQNVGFGLKVKGTPKAAIDKRVEEMLSLIGLPD-LGNRYP 131

Query: 131 FELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLTTILVT 190
           F+LSGGQ +RVA+A  LA  P VL+LDEP + LD + R  + +    + +   +TTI VT
Sbjct: 132 FQLSGGQQQRVALARALAPKPSVLLLDEPLSALDAKVRVSLRNEIRAIQRELGITTIFVT 191

Query: 191 HSMEDAAAYADEMIVMHKGTIQASGSPRDLF 221
           H  E+A + +D ++VMH+G     G+P D++
Sbjct: 192 HDQEEALSMSDRVVVMHEGIADQVGTPFDIY 222


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: 222
Number of extensions: 14
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: 276
Length of database: 348
Length adjustment: 27
Effective length of query: 249
Effective length of database: 321
Effective search space:    79929
Effective search space used:    79929
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 24 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