GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA1 in Bacillus altitudinis 41KF2b

Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate WP_017368436.1 BA79_RS17265 ABC transporter ATP-binding protein

Query= uniprot:P40735
         (281 letters)



>NCBI__GCF_000691145.1:WP_017368436.1
          Length = 571

 Score =  169 bits (429), Expect = 1e-46
 Identities = 98/236 (41%), Positives = 140/236 (59%), Gaps = 10/236 (4%)

Query: 6   LISVEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPES-- 63
           +I  E   F+YR  AE    D V+L +YEGE + I G +GSGKSTLA  +NGL+ P S  
Sbjct: 5   MIQFEHFGFKYRSQAEPTLKD-VNLTIYEGEKVLIAGPSGSGKSTLAHCINGLV-PASYK 62

Query: 64  ----GDIEVAGIQLTEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEM 119
               G + + G    +E+++ + + +G V Q+PD QF+G TV +D+AF LEN+ V REEM
Sbjct: 63  GSMEGSLHIGGKNAEKENIFSLSQLVGTVLQDPDGQFIGLTVGEDIAFTLENDQVTREEM 122

Query: 120 IERVDWAVKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGRE 179
             RV+ A K   +   L    H LSGGQKQRVAIAGV+    DI++ DE  + LDP   +
Sbjct: 123 KTRVEKAAKLTEVDGKLASSVHELSGGQKQRVAIAGVLVNDVDILLFDEPLASLDPATGK 182

Query: 180 EVLETVRHLKEQGMATVISITHDLNEA--AKADRIIVMNGGKKYAEGPPEEIFKLN 233
           EV++ +  L+++   TV+ + H L +      DRIIV+N G   A+  P+E+   N
Sbjct: 183 EVIDLIDRLQKETKKTVVMVEHRLEDVLFRHVDRIIVVNDGTIAADMTPDELLASN 238



 Score =  124 bits (311), Expect = 5e-33
 Identities = 74/225 (32%), Positives = 127/225 (56%), Gaps = 4/225 (1%)

Query: 6   LISVEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGD 65
           L+ V ++ F Y        L+ +S  V +GE ++I G NG+GK+TL++ L     P  G 
Sbjct: 302 LLEVRELSFDY--PTRPNTLNNISFTVKKGEMISIAGANGAGKTTLSKVLCAFEKPTKGT 359

Query: 66  IEVAGIQLTEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDW 125
           I + G  +T +++ +  ++IG+V QNP+       + D+VA GL   GV  +++ +RV+ 
Sbjct: 360 IHLNGDDITGDTIKQRSERIGVVMQNPNQMISKQMIFDEVALGLVLRGVKEDDIKDRVER 419

Query: 126 AVKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETV 185
            +K   +  F +     LS GQK+RV IA ++   P+IIILDE T+  D     E++  +
Sbjct: 420 VLKVCGLYPFRNWPISALSFGQKKRVTIASILVLEPEIIILDEPTAGQDFRHYTEMMTFL 479

Query: 186 RHLKEQGMATVISITHDLNEAAK-ADRIIVMNGGKKYAEGPPEEI 229
             L +QG+ T++ ITHD++   +   R IV++ G+K A+  P ++
Sbjct: 480 EQLNQQGV-TILMITHDMHLMLEYTTRTIVISDGEKIADDTPAKV 523


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: 428
Number of extensions: 20
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 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