GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA1 in Rhizorhabdus wittichii RW1

Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein

Query= uniprot:P40735
         (281 letters)



>NCBI__GCF_000016765.1:WP_041378948.1
          Length = 252

 Score =  139 bits (349), Expect = 8e-38
 Identities = 85/212 (40%), Positives = 125/212 (58%), Gaps = 3/212 (1%)

Query: 20  AERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTEESVW 79
           A R  LD VSL +  G ++A+VG +G+GK+TL +A+N L+  ++G I + G  +  + V 
Sbjct: 12  AGRHVLDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAIEGRDVAAQPVA 71

Query: 80  EVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVKQVNMQ-DFLDQ 138
           E+R++IG VFQ     F   +V ++VA      GVPREE   RV   +  V +  DF ++
Sbjct: 72  ELRRRIGYVFQGI-GLFPHMSVAENVALVPRLQGVPREERAARVAELLDLVALPADFAER 130

Query: 139 EPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQGMATVIS 198
            P  LSGGQ QRV  A  +AARP I+++DE    LDP+ R+E+    R L E    T + 
Sbjct: 131 RPAQLSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYRALHEAMGLTSLI 190

Query: 199 ITHDLNEA-AKADRIIVMNGGKKYAEGPPEEI 229
           +THD+ EA   ADR+IV+  G+  A+ PP  +
Sbjct: 191 VTHDMAEALLLADRVIVIGEGRILADQPPRAL 222


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: 147
Number of extensions: 8
Number of successful extensions: 4
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: 252
Length adjustment: 25
Effective length of query: 256
Effective length of database: 227
Effective search space:    58112
Effective search space used:    58112
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 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