GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA1 in Paucidesulfovibrio gracilis DSM 16080

Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate WP_200806763.1 B5D49_RS03200 ABC transporter ATP-binding protein

Query= uniprot:P40735
         (281 letters)



>NCBI__GCF_900167125.1:WP_200806763.1
          Length = 406

 Score =  134 bits (336), Expect = 4e-36
 Identities = 74/208 (35%), Positives = 125/208 (60%), Gaps = 4/208 (1%)

Query: 24  ALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTEESVWEVRK 83
           A+    L +  GE + ++G +G GK+T+ R + GL  P  GDI + G ++ +  +   ++
Sbjct: 59  AVQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGDIYIKGRRINDTPIH--KR 116

Query: 84  KIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVKQVNMQDFLDQEPHHL 143
            +GM+FQN    F   T+ ++VAFGL+   V REEM E+V  A++ V +     +    L
Sbjct: 117 NLGMIFQNYA-LFPHKTIFENVAFGLKYRNVSREEMREKVAQALEMVRLPGVEKRYASQL 175

Query: 144 SGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQGMATVISITHDL 203
           SGGQ+QR+A+A  I   PD++++DE  S LD   REE+   + ++++Q   T + +THD 
Sbjct: 176 SGGQQQRIALARAIVIEPDVLLMDEPLSALDEKLREEMRMEIDNIQQQLNLTTLFVTHDQ 235

Query: 204 NEA-AKADRIIVMNGGKKYAEGPPEEIF 230
            EA + +++I+VM  G+K  EG PE+++
Sbjct: 236 REALSMSNKIVVMKDGRKQQEGTPEDVY 263


Lambda     K      H
   0.316    0.135    0.383 

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: 267
Number of extensions: 18
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: 281
Length of database: 406
Length adjustment: 28
Effective length of query: 253
Effective length of database: 378
Effective search space:    95634
Effective search space used:    95634
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 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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