GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xacK in Marinobacter adhaerens HP15

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF1380 HP15_1347 sulfate/thiosulfate transporter subunit

Query= uniprot:D4GP39
         (383 letters)



>lcl|FitnessBrowser__Marino:GFF1380 HP15_1347 sulfate/thiosulfate
           transporter subunit
          Length = 362

 Score =  209 bits (532), Expect = 1e-58
 Identities = 119/304 (39%), Positives = 179/304 (58%), Gaps = 16/304 (5%)

Query: 23  AVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQDRDI 82
           A+ +I+L I DG+   L+GPSG GK+T LR++AGLET  EG +R   + +  +  +DR +
Sbjct: 17  ALHDINLTIPDGQLTALLGPSGSGKTTLLRIIAGLETPEEGRIRFSGKDVTDLHVRDRRV 76

Query: 83  AMVFQSYALYPHKSVRGNMSFGL-----EESTGLPDDEIRQRVEETTDMLGISDLLDRKP 137
             VFQ YAL+ H +V  N++FGL     +E  G P  EIR+RV++  +M+ +  L DR P
Sbjct: 77  GFVFQHYALFRHMTVAENVAFGLNVLPRKERPGKP--EIRKRVKDLLEMVQLEHLADRYP 134

Query: 138 GQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYVT 197
            QLSGGQ+QR+AL RA+   PE+ L+DEP   LDAK+R ++R  L+ L  EL  T+V+VT
Sbjct: 135 AQLSGGQKQRIALARAMAMRPEILLLDEPFGALDAKVRKDLRRWLRSLHDELHFTSVFVT 194

Query: 198 HDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGSLSGDTF 257
           HDQ EA+ + D+V V+ +G ++QV TPL+ Y RP++ FV  F+G+  +N+  G +     
Sbjct: 195 HDQEEALELSDQVVVMSNGRIEQVDTPLELYGRPDSRFVFEFLGQ--VNVLSGKIRDGVM 252

Query: 258 R-GDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQRTFDAEVVVVEPQGNENA 316
           R GD +     G   D         L +RP +V + +  S        +  +   G E  
Sbjct: 253 RQGDAWIRLPEGCENDD------AQLYLRPHEVRLTQSASDDAHLPFRIEAINLIGAEVR 306

Query: 317 VHLR 320
           + L+
Sbjct: 307 IELK 310


Lambda     K      H
   0.316    0.136    0.384 

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: 372
Number of extensions: 17
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: 383
Length of database: 362
Length adjustment: 30
Effective length of query: 353
Effective length of database: 332
Effective search space:   117196
Effective search space used:   117196
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: 42 (22.0 bits)
S2: 49 (23.5 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 paper from 2022 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