GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Marinobacter adhaerens HP15

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate GFF1380 HP15_1347 sulfate/thiosulfate transporter subunit

Query= uniprot:D8IPI1
         (406 letters)



>FitnessBrowser__Marino:GFF1380
          Length = 362

 Score =  213 bits (542), Expect = 7e-60
 Identities = 127/303 (41%), Positives = 181/303 (59%), Gaps = 23/303 (7%)

Query: 20  LHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARERNVA 79
           LH ++L I DG+   LLGPSG GK+T+LR+IAGLE    G +R  G  V DL  R+R V 
Sbjct: 18  LHDINLTIPDGQLTALLGPSGSGKTTLLRIIAGLETPEEGRIRFSGKDVTDLHVRDRRVG 77

Query: 80  MVFQNYALYPHMSVYDNIAFGLR---RLKRPAA-EIDRRVREVAALLNLEALLERKPRAM 135
            VFQ+YAL+ HM+V +N+AFGL    R +RP   EI +RV+++  ++ LE L +R P  +
Sbjct: 78  FVFQHYALFRHMTVAENVAFGLNVLPRKERPGKPEIRKRVKDLLEMVQLEHLADRYPAQL 137

Query: 136 SGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQ 195
           SGGQ+QR A+ARA+   P + L DEP   LDAK+R  LR  ++ LH  L  T+V+VTHDQ
Sbjct: 138 SGGQKQRIALARAMAMRPEILLLDEPFGALDAKVRKDLRRWLRSLHDELHFTSVFVTHDQ 197

Query: 196 LEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDGQLF 255
            EA+ L+D+V++M +GRI Q  +P ELY  P + F   F+G   +N LSG +  +DG + 
Sbjct: 198 EEALELSDQVVVMSNGRIEQVDTPLELYGRPDSRFVFEFLG--QVNVLSGKI--RDGVM- 252

Query: 256 IETAHQRWALTGERFSRLRHAMA---VKLAVRPDHVRIAGEREPAASLTCPVSVELVEIL 312
                      G+ + RL         +L +RP  VR+       A L  P  +E + ++
Sbjct: 253 ---------RQGDAWIRLPEGCENDDAQLYLRPHEVRLTQSASDDAHL--PFRIEAINLI 301

Query: 313 GAD 315
           GA+
Sbjct: 302 GAE 304


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: 11
Number of successful extensions: 2
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: 362
Length adjustment: 30
Effective length of query: 376
Effective length of database: 332
Effective search space:   124832
Effective search space used:   124832
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:

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