GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Korea:Ga0059261_3276 Ga0059261_3276 ABC-type
           multidrug transport system, ATPase and permease
           components
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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