GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA1 in Burkholderia phytofirmans PsJN

Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate BPHYT_RS22535 BPHYT_RS22535 methionine ABC transporter ATP-binding protein

Query= uniprot:P40735
         (281 letters)



>FitnessBrowser__BFirm:BPHYT_RS22535
          Length = 386

 Score =  135 bits (339), Expect = 2e-36
 Identities = 82/222 (36%), Positives = 125/222 (56%), Gaps = 5/222 (2%)

Query: 13  VFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGI- 71
           VF   +     AL  V+L V  GE   I+G +G+GKSTL R +NGL  P SG + V G+ 
Sbjct: 40  VFADARGVSTAALANVTLNVARGEVFGIIGRSGAGKSTLLRLVNGLEKPSSGAVRVNGVS 99

Query: 72  --QLTEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVKQ 129
             +L E  +  +R++IGMVFQ+  N     TVR+++A  L+  GVP+  + ++VD  ++ 
Sbjct: 100 VGELDERGLVALRRRIGMVFQH-FNLLSAKTVRENIALPLKIAGVPKAAIDKKVDALLEL 158

Query: 130 VNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLK 189
           V +    D  P  LSGGQKQRV IA  +   PDI++ DEATS LDP   + +L  +R + 
Sbjct: 159 VGLSAKRDAYPASLSGGQKQRVGIARALVTDPDILLCDEATSALDPETTQAILALLRDIN 218

Query: 190 EQGMATVISITHDLNEAAK-ADRIIVMNGGKKYAEGPPEEIF 230
           ++   T++ ITH++    +  D + V+  G+    G    +F
Sbjct: 219 QRLNLTIVLITHEMQVIREVCDTVAVIERGEVVETGAVWRVF 260


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: 250
Number of extensions: 13
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: 386
Length adjustment: 28
Effective length of query: 253
Effective length of database: 358
Effective search space:    90574
Effective search space used:    90574
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: 49 (23.5 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