GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS17020 in Synechococcus elongatus PCC 7942

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase

Query= uniprot:D8IPI1
         (406 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_0960 Synpcc7942_0960 ATPase
          Length = 417

 Score =  287 bits (735), Expect = 4e-82
 Identities = 165/369 (44%), Positives = 224/369 (60%), Gaps = 31/369 (8%)

Query: 19  VLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARERNV 78
           VL+ ++L I DGEF+V++GPSGCGKST+LR++AGLE  S G +++G   V+ LPA+ R++
Sbjct: 49  VLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAGLETPSRGLIKVGDRRVDRLPAKARDI 108

Query: 79  AMVFQNYALYPHMSVYDNIAFGLRRL-KRP-----------------------AAEIDRR 114
           AMVFQ+YALYPH+SVYDN+AFGLRR   RP                        A I RR
Sbjct: 109 AMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQQLALATRSLPKSLQYEPEQEARIKRR 168

Query: 115 VREVAALLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLR 174
           VREVA +L L+ LL+R+P+ +SGGQ+QR A+ RAI + P VFL DEPLSNLDAKLRA+ R
Sbjct: 169 VREVATMLQLDTLLDRQPKQLSGGQKQRVALGRAIARNPQVFLMDEPLSNLDAKLRAETR 228

Query: 175 GDIKRLHQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGF 234
             I  L ++L  TT+YVTHDQ EAMT+ DR+ ++  G + Q  SP E+Y  P N F A F
Sbjct: 229 AQIVSLQRQLGVTTLYVTHDQTEAMTMGDRIAVLNRGHLQQVASPLEIYDRPANRFVAQF 288

Query: 235 IGTPAMNFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGER 294
           IG+P MN +  TV R   QL  E          E   RL     V+L +RP+H+ +    
Sbjct: 289 IGSPPMNLIPVTV-RAPLQLTTENFRCTLPEAWEPVLRLYDGQTVELGIRPEHLEVGA-- 345

Query: 295 EPAASLTCPVSVELVEILGADALLTTRCGDQ--TLTALVPADRLPQPGATLTLALDQHEL 352
             AAS    ++V  VE LG+D  +     +    + A +   +  Q G  L L     ++
Sbjct: 346 --AASKNLLITVTGVEALGSDTFIAGELKESGIAVQARLAPQQCWQMGDRLWLTFKPDQI 403

Query: 353 HVFDVESGE 361
           H+FD+E+G+
Sbjct: 404 HLFDLETGK 412


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: 406
Number of extensions: 16
Number of successful extensions: 4
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: 417
Length adjustment: 31
Effective length of query: 375
Effective length of database: 386
Effective search space:   144750
Effective search space used:   144750
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 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 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