GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ecfA1 in Shewanella sp. ANA-3

Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)

Query= uniprot:P40735
         (281 letters)



>lcl|FitnessBrowser__ANA3:7026050 Shewana3_3192 sulfate ABC
           transporter, ATPase subunit (RefSeq)
          Length = 376

 Score =  123 bits (308), Expect = 7e-33
 Identities = 76/219 (34%), Positives = 126/219 (57%), Gaps = 8/219 (3%)

Query: 17  RKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTEE 76
           +K  + +AL  ++L + EGE + ++G +GSGK+TL R + GL   +SG I      +T+ 
Sbjct: 10  KKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIHFGNRDVTQV 69

Query: 77  SVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLE----NNGVPREEMIERVDWAVKQVNM 132
            V +  +++G VFQN    F   TV D+VAFGLE         + E+ +RV   ++ V +
Sbjct: 70  HVRD--RRVGFVFQNYA-LFRHMTVADNVAFGLEVIPKKQRPSKAEIQKRVSHLLEMVQL 126

Query: 133 QDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQG 192
                + P  LSGGQKQR+A+A  +A +P++++LDE    LD   R+E+   +R L ++ 
Sbjct: 127 GHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWLRSLHDEL 186

Query: 193 MATVISITHDLNEAAK-ADRIIVMNGGKKYAEGPPEEIF 230
             T + +THD +EA + +DR++VM+ G       P E++
Sbjct: 187 KFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELY 225


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: 272
Number of extensions: 14
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: 376
Length adjustment: 28
Effective length of query: 253
Effective length of database: 348
Effective search space:    88044
Effective search space used:    88044
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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