GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Thiothrix lacustris DSM 21227

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein

Query= uniprot:D8IPI1
         (406 letters)



>NCBI__GCF_000621325.1:WP_028489030.1
          Length = 348

 Score =  259 bits (662), Expect = 8e-74
 Identities = 146/321 (45%), Positives = 199/321 (61%), Gaps = 28/321 (8%)

Query: 1   MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60
           MA +  + + K+Y G    +  + L I  GEF+V +GPSGCGKST+LRMIAGLE I+GG 
Sbjct: 1   MAFLELKNVDKYY-GKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQ 59

Query: 61  LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120
           L + G  + ++P  +R++AMVFQ+YALYPHM+V +N++F LR  K   A I  +V+  A 
Sbjct: 60  LILDGRDITEVPPSQRDLAMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAAD 119

Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180
            LNL A L+R P+A+SGGQ+QR AI R+I+++P VFLFDEPLSNLDA LR   R +I  L
Sbjct: 120 KLNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIASL 179

Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240
           H+ L  TTVYVTHDQ+EAMTLADRV++++DG I Q G+P ELY  P N F A FIG P M
Sbjct: 180 HRELGATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFVARFIGMPQM 239

Query: 241 NFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASL 300
           N    ++  Q                         A   ++ +RP+H+++    +   + 
Sbjct: 240 NVAPASLFGQ-----------------------FPAQVAEVGIRPEHLQMVSPEDGLLA- 275

Query: 301 TCPVSVELVEILGADALLTTR 321
                V LVE LG + L+  R
Sbjct: 276 ---GKVVLVEALGNETLVHVR 293


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: 364
Number of extensions: 18
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: 348
Length adjustment: 30
Effective length of query: 376
Effective length of database: 318
Effective search space:   119568
Effective search space used:   119568
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