GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA1 in Desulfacinum hydrothermale DSM 13146

Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate WP_170920503.1 B9A12_RS09210 energy-coupling factor transporter ATPase

Query= uniprot:P40735
         (281 letters)



>NCBI__GCF_900176285.1:WP_170920503.1
          Length = 571

 Score =  153 bits (386), Expect = 1e-41
 Identities = 91/228 (39%), Positives = 135/228 (59%), Gaps = 5/228 (2%)

Query: 22  RRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTEESVWEV 81
           R+AL  + L ++EGE +A++GHNGSGK+TLAR L+GL  P  G +   G  L+ E + ++
Sbjct: 32  RQALRHIDLSIHEGERIAVLGHNGSGKTTLARVLSGLAPPTQGRVLFQGDPLSRERLEDL 91

Query: 82  RKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVKQVNMQDFLDQEPH 141
           R+++G +FQ+PD+Q    TV DDV FGL N  VP +E  ER   A+  + ++    + PH
Sbjct: 92  RQRVGFLFQDPDDQLFCPTVLDDVLFGLLNFQVPPKEAEERARKALAAMGLEAEAHRAPH 151

Query: 142 HLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQGMATVISITH 201
           HLS GQ++R A+A ++A  PD++ILDE T+ +DP   E +L  V  LK+    T+I I+H
Sbjct: 152 HLSYGQRKRAALAAILALEPDVLILDEPTANMDPTS-EALLSKV--LKDY-PGTLICISH 207

Query: 202 D-LNEAAKADRIIVMNGGKKYAEGPPEEIFKLNKELVRIGLDLPFSFQ 248
           D L       R +V+  G  + +   E +      L   GLD  F FQ
Sbjct: 208 DILFLYGLCTRAVVLQAGGIHHDTSFERLISHRASLQEHGLDFTFRFQ 255



 Score =  125 bits (314), Expect = 2e-33
 Identities = 87/260 (33%), Positives = 149/260 (57%), Gaps = 12/260 (4%)

Query: 9   VEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEV 68
           +E + F Y       AL+ VS QV  GE LA+VG NG+GKSTLA  L G I   +G   +
Sbjct: 312 LEMLGFSYAYGDGTVALENVSFQVGRGERLALVGPNGAGKSTLAACLAG-IRWGTGQYLL 370

Query: 69  AGIQLTEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVK 128
            G ++       + + +G+VFQ+  +Q V +   D+VAFGL N G P   + ++V   + 
Sbjct: 371 DGRKVEGAFRRNLWRHVGLVFQDSADQMVCSRCGDEVAFGLRNLGWPESRIRKKVQAMLH 430

Query: 129 QVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHL 188
              ++ F D+ P HLSGG+++R+A+A V+A  P+++ILDE T+ LDP   +++L+    L
Sbjct: 431 WAGLEGFEDRVPQHLSGGERKRLALAAVLAMEPEVLILDEPTAGLDPQTEQKLLQ----L 486

Query: 189 KEQGMATVISITHDLNEAAK-ADRIIVMNGGKKYAEGPPEEIFKLNKELVRI-GLDLPFS 246
            ++  AT++ I+HD+   +   DR ++M+ G +  +  P   F +++ L  + GLD  + 
Sbjct: 487 LDEVEATLVLISHDVCFVSMLTDRTLLMHRG-RIVDDLPTGKFLVDRNLHSLYGLDFTYY 545

Query: 247 FQLSQLLRENGLALEENHLT 266
            +  + +++    L+E+H T
Sbjct: 546 NRCCREIQD----LQEDHRT 561


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: 396
Number of extensions: 25
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 281
Length of database: 571
Length adjustment: 31
Effective length of query: 250
Effective length of database: 540
Effective search space:   135000
Effective search space used:   135000
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: 50 (23.9 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