GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Methanosarcina acetivorans C2A

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_011020381.1 MA_RS01715 ATP-binding cassette domain-containing protein

Query= uniprot:D8IPI1
         (406 letters)



>NCBI__GCF_000007345.1:WP_011020381.1
          Length = 353

 Score =  177 bits (450), Expect = 3e-49
 Identities = 94/273 (34%), Positives = 160/273 (58%), Gaps = 6/273 (2%)

Query: 20  LHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARERNVA 79
           L  +DL    G++V L+GPSG GKS +L  I G      G++ + G  +      +R ++
Sbjct: 18  LKGIDLRAEKGDYVALIGPSGSGKSLLLETIIGFYGPRQGSVFLEGRDITFFSPDKRQIS 77

Query: 80  MVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRAMSGGQ 139
           +V+Q+  L+PHM +++NIA+ LR+  +   +I+  V ++A +L +  LL RKP  +SGG+
Sbjct: 78  IVYQDNMLFPHMDIFENIAYALRKKLKDKKQIELEVTQIAGVLGIRELLHRKPDTLSGGE 137

Query: 140 QQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQLEAM 199
           +QRA++AR+++  P + L DEP S LDA+ R +LR  +K+      TT ++VTHD  +  
Sbjct: 138 KQRASLARSLVARPKLLLLDEPFSALDARTREKLREMLKKAIADYSTTVLHVTHDFEDVW 197

Query: 200 TLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDGQLFIETA 259
            LA+RV++++ G ++Q G P  ++R P   F A F+GT   N L GTV+  +G+L +  A
Sbjct: 198 ALANRVVVIRKGEVMQVGDPESVFRRPSPDFVAEFLGT---NVLKGTVKALEGKLTVIDA 254

Query: 260 HQRWALTGERFSRLRHAMAVKLAVRPDHVRIAG 292
                 + +          V +++RP+ + +AG
Sbjct: 255 EGMEIYSAD---PAEPGENVTVSIRPEEIILAG 284


Lambda     K      H
   0.321    0.137    0.403 

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: 293
Number of extensions: 10
Number of successful extensions: 1
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: 406
Length of database: 353
Length adjustment: 30
Effective length of query: 376
Effective length of database: 323
Effective search space:   121448
Effective search space used:   121448
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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