GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA1 in Methanobacterium arcticum M2

Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate WP_048082401.1 EI99_RS13040 ATP-binding cassette domain-containing protein

Query= uniprot:P40735
         (281 letters)



>NCBI__GCF_000746075.1:WP_048082401.1
          Length = 279

 Score =  174 bits (440), Expect = 3e-48
 Identities = 94/253 (37%), Positives = 160/253 (63%), Gaps = 6/253 (2%)

Query: 6   LISVEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGD 65
           +I  +++ ++Y       AL+ ++     G+ +A++G NG+GKSTL    NG++ P SG 
Sbjct: 3   IIETKNVTYQYPDGTN--ALENINFSAPTGKIIALLGPNGAGKSTLFLHFNGILQPTSGS 60

Query: 66  IEV--AGIQLTEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERV 123
           + V  A +   +E +  +R+K+G+VFQNPD+Q    TV +DVAFG  N G+ +EE+ +RV
Sbjct: 61  VMVDNACLNYKKEDLMNLRQKVGIVFQNPDDQLFAPTVVEDVAFGPVNLGLSKEEVKKRV 120

Query: 124 DWAVKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLE 183
           D ++++V M +F  + PHHLSGGQK+RVAIAG++A  P I++LDE TS LDP G  ++++
Sbjct: 121 DESLRRVEMIEFKHKAPHHLSGGQKKRVAIAGILAMHPKIMVLDEPTSGLDPRGASKIMK 180

Query: 184 TVRHLKEQGMATVISITHDLN-EAAKADRIIVMNGGKKYAEGPPEEIFKLNKELVRIGLD 242
            +  L  +G+  +IS THD++     A  + +++ G    +G P+E+F+  + + +  L 
Sbjct: 181 LLYELNREGITIIIS-THDVDLVPLYAHSVYIISKGNIIKKGSPQEVFEDAETIRKANLR 239

Query: 243 LPFSFQLSQLLRE 255
           LP    L ++L++
Sbjct: 240 LPRIAHLVEILQK 252


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: 191
Number of extensions: 9
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: 279
Length adjustment: 26
Effective length of query: 255
Effective length of database: 253
Effective search space:    64515
Effective search space used:    64515
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: 47 (22.7 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