GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA1 in Escherichia coli BW25113

Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate 14980 b0855 ATP-binding component of putrescine transport system (VIMSS)

Query= uniprot:P40735
         (281 letters)



>FitnessBrowser__Keio:14980
          Length = 377

 Score =  142 bits (358), Expect = 1e-38
 Identities = 85/211 (40%), Positives = 128/211 (60%), Gaps = 4/211 (1%)

Query: 22  RRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTEESVWEV 81
           + A+D VSL +Y+GE  A++G +G GKSTL R L G   P +G I + G+ L++  V   
Sbjct: 32  QHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIMLDGVDLSQ--VPPY 89

Query: 82  RKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVKQVNMQDFLDQEPH 141
            + I M+FQ+    F   TV  ++AFGL+ + +P+ E+  RV+  +  V+MQ+F  ++PH
Sbjct: 90  LRPINMMFQSYA-LFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLVHMQEFAKRKPH 148

Query: 142 HLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQGMATVISITH 201
            LSGGQ+QRVA+A  +A RP +++LDE    LD   R+ +   V  + E+   T + +TH
Sbjct: 149 QLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILERVGVTCVMVTH 208

Query: 202 DLNEA-AKADRIIVMNGGKKYAEGPPEEIFK 231
           D  EA   A RI +MN GK    G PEEI++
Sbjct: 209 DQEEAMTMAGRIAIMNRGKFVQIGEPEEIYE 239


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: 255
Number of extensions: 17
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: 377
Length adjustment: 28
Effective length of query: 253
Effective length of database: 349
Effective search space:    88297
Effective search space used:    88297
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