GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA1 in Sphingomonas koreensis DSMZ 15582

Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate Ga0059261_3276 Ga0059261_3276 ABC-type multidrug transport system, ATPase and permease components

Query= uniprot:P40735
         (281 letters)



>FitnessBrowser__Korea:Ga0059261_3276
          Length = 595

 Score =  108 bits (270), Expect = 3e-28
 Identities = 82/235 (34%), Positives = 116/235 (49%), Gaps = 23/235 (9%)

Query: 7   ISVEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDI 66
           I  +++ FRY    E  AL   +L V  GE +A+VG +G+GKSTL + +     PE G+I
Sbjct: 353 IDFKNVTFRYPTRPEVSALHQFTLSVAPGETVAVVGPSGAGKSTLFQLVQRFYDPEGGEI 412

Query: 67  EVAGIQLTEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDW- 125
            V GI +      EVR ++ MV Q  +      T RD++ +G       R +  E   W 
Sbjct: 413 RVDGIPVRSADPGEVRARMAMVPQ--ETVIFAATARDNLRYG-------RWDATEEQIWQ 463

Query: 126 AVKQVNMQDFLDQEPH-----------HLSGGQKQRVAIAGVIAARPDIIILDEATSMLD 174
           A +  N  +FL + P             LSGGQ+QR+AIA  +     I++LDEATS LD
Sbjct: 464 AAEAANAAEFLRELPQGLETFLGEDGARLSGGQRQRLAIARALLRDAPILLLDEATSALD 523

Query: 175 PIGREEVLETVRHLKEQGMATVISITHDLNEAAKADRIIVMNGGKKYAEGPPEEI 229
                 V + + HL  QG  T++ I H L     A RIIVM+ G+    G   E+
Sbjct: 524 AESERLVQDALEHLM-QGRTTLV-IAHRLATVRAAKRIIVMDEGRIVETGTHAEL 576


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: 326
Number of extensions: 20
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: 595
Length adjustment: 31
Effective length of query: 250
Effective length of database: 564
Effective search space:   141000
Effective search space used:   141000
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 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