GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylT in Kocuria flava HO-9041

Align D-xylose transporter; D-xylose-proton symporter (characterized)
to candidate WP_058858199.1 AS188_RS06680 sugar porter family MFS transporter

Query= SwissProt::O52733
         (457 letters)



>NCBI__GCF_001482365.1:WP_058858199.1
          Length = 482

 Score =  275 bits (704), Expect = 2e-78
 Identities = 161/444 (36%), Positives = 260/444 (58%), Gaps = 14/444 (3%)

Query: 7   GFVYFFGALGGLLFGYDTGVISGAILFIQKQMNLGSWQQGWVVSAVLLGAILGAAIIGPS 66
           G +      GGLLFGYDTGVI+GA+  + +++ L  + +G V S+++  A +GA   G  
Sbjct: 27  GLISIVACFGGLLFGYDTGVINGALRPMTEELGLTPFTEGVVTSSLVFAAAVGALSGGRI 86

Query: 67  SDRFGRRKLLLLSAIIFFVGALGSAFSPEFWTLIISRIILGMAVGAASALIPTYLAELAP 126
           SD +GRR+ +LL A++FFVG +   F+P +  L+  R+ LG+AVG ASA++P +LAELAP
Sbjct: 87  SDAWGRRRTILLLAVLFFVGTMIVVFTPNYEVLVAGRVCLGLAVGGASAVVPVFLAELAP 146

Query: 127 SDKRGTVSSLFQLMVMTGILLAYITNYSFSGFY----TGWRWMLGFAAIPAALLFLGGLI 182
            + RG+++   ++ ++ G L A++ N      +    + WR+M   +A+PA  LF+G L 
Sbjct: 147 YEIRGSIAGRNEVAIVIGQLSAFVINAVIGNVFIDHPSVWRYMFAISALPAVALFVGMLR 206

Query: 183 LPESPRFLVKSGHLDEARHVLDTMNKHDQ-VAVNKEINDI--QESAKIVSGGWSELFGKM 239
           +PESPR+LV+ G  +EA  VL ++   ++ VA   E+  +  +ESA+   G  + L  K 
Sbjct: 207 MPESPRWLVEKGRHEEALEVLRSVRSEERAVAELGEVEHVAEEESAENRIGLGAVLRNKW 266

Query: 240 VRPSLIIGIGLAIFQQVMGCNTVLYYAPTIFTDVGFGVSAALLAHIGIGIFNVIVTAIAV 299
           +   +++GIGL I QQ+ G N+++YY   +  + GF  SAAL+A+I  G+  V+   IA+
Sbjct: 267 LIRIMLVGIGLGIAQQLTGINSIMYYGQIVLIESGFSASAALIANIAPGVIAVVGGFIAL 326

Query: 300 AIMDKIDRKKIVNIG-AVGMGISLFVMSIGMKFSGGSQTAAIISVIALTVYIAFFSATWG 358
           A+MD++DR+K   IG ++     L +    +    G+     + +  +  ++        
Sbjct: 327 AMMDRLDRRKTFVIGFSLTTTCHLLIGIASVVLEEGNPLRPFVILALVVAFVGSMQTFLN 386

Query: 359 PVMWVMIGEVFPLNIRGLGNSFASVINWTANMIVSLTFPSLLD---FFGTGSLFIGYGIL 415
             +WV + EVFPL++RG G   +    W AN ++SL FPSL+D     GT  LF G G+L
Sbjct: 387 VAVWVYLSEVFPLHMRGFGIGVSIFALWVANGVLSLYFPSLVDAVGITGTFFLFAGVGVL 446

Query: 416 CFASIWFVQKKVFETRNRSLEDIE 439
              ++ FV  +V ETR R+LE +E
Sbjct: 447 ---ALVFVATQVPETRGRTLEALE 467


Lambda     K      H
   0.327    0.141    0.424 

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: 572
Number of extensions: 41
Number of successful extensions: 5
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: 457
Length of database: 482
Length adjustment: 33
Effective length of query: 424
Effective length of database: 449
Effective search space:   190376
Effective search space used:   190376
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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