GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA1 in Marinobacter adhaerens HP15

Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate GFF4127 HP15_4067 spermidine/putrescine ABC transporter ATPase subunit

Query= uniprot:P40735
         (281 letters)



>FitnessBrowser__Marino:GFF4127
          Length = 362

 Score =  134 bits (336), Expect = 4e-36
 Identities = 82/223 (36%), Positives = 131/223 (58%), Gaps = 7/223 (3%)

Query: 10  EDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVA 69
           E +V R+  +A   A+D VSL V  G + +I+G +G GK+TL R L G   P+ GDI + 
Sbjct: 8   EGLVRRFGSNA---AVDHVSLDVPAGTFFSILGPSGCGKTTLLRLLAGFDKPDQGDIHIR 64

Query: 70  GIQLTEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVKQ 129
           G ++ +  V   R+ + MVFQ+    F   TV D++A+GL+   +P  E  +R+   ++Q
Sbjct: 65  GERMND--VPPNRRPVNMVFQHLA-LFPTMTVGDNIAYGLKRRKMPLVERRKRIARVLEQ 121

Query: 130 VNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLK 189
           V + D   + P  LSGGQ+QRVA+A  +   P +++LDE    LD   RE++   ++HL+
Sbjct: 122 VGLPDLEHRNPQELSGGQRQRVALARCLVLEPTLLLLDEPLGALDLKLREQMKVELKHLQ 181

Query: 190 EQGMATVISITHDLNEA-AKADRIIVMNGGKKYAEGPPEEIFK 231
           +Q   T + ITHD +EA   +D++ VM  G+     PPEE+++
Sbjct: 182 KQFGTTFVYITHDQSEAMVMSDQVAVMRDGRFDQVAPPEELYR 224


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: 224
Number of extensions: 13
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: 362
Length adjustment: 27
Effective length of query: 254
Effective length of database: 335
Effective search space:    85090
Effective search space used:    85090
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: 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