GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylT in Tatumella morbirosei LMG 23360

Align D-xylose transporter; D-xylose-proton symporter (characterized)
to candidate WP_038022443.1 HA49_RS09585 sugar porter family MFS transporter

Query= SwissProt::O52733
         (457 letters)



>NCBI__GCF_000757425.2:WP_038022443.1
          Length = 501

 Score =  264 bits (674), Expect = 6e-75
 Identities = 154/434 (35%), Positives = 239/434 (55%), Gaps = 6/434 (1%)

Query: 14  ALGGLLFGYDTGVISGAILFIQKQMNLGSWQQGWVVSAVLLGAILGAAIIGPSSDRFGRR 73
           A+ G L+GYDTG+ISGA+L I    +L    Q  V SA+L+GA++GA + G  S   GRR
Sbjct: 46  AIAGFLYGYDTGIISGALLQISHDFSLSGQAQELVTSAILVGAVIGALVCGKLSATIGRR 105

Query: 74  KLLLLSAIIFFVGALGSAFSPEFWTLIISRIILGMAVGAASALIPTYLAELAPSDKRGTV 133
             ++  A IF +G L S +S     L ++R++LG AVG AS ++P Y+AELAPS KRG +
Sbjct: 106 YTVMTVAAIFAIGVLASGWSDSATALALARVVLGFAVGGASQIVPVYIAELAPSHKRGRL 165

Query: 134 SSLFQLMVMTGILLAYITNYSFSGFYTGWRWMLGFAAIPAALLFLGGLILPESPRFLVKS 193
            + F + +  GIL A +        ++ WR M   AAIPA +L  G L LPESPR+LV  
Sbjct: 166 VTFFNISIGVGILTAGLVGAFLQDIWS-WRVMFSVAAIPALILMFGMLPLPESPRWLVGQ 224

Query: 194 GHLDEARHVLDTMNKHDQVAVNKEINDIQ----ESAKIVSGGWSELFGKMVRPSLIIGIG 249
               EAR  L+ + + D+  V  E+ +IQ    ++A+  + GW +L    +RP+L  G+G
Sbjct: 225 KRTREARIALNMVRETDR-EVRHELRNIQKVHDKTARKSTLGWKDLKQPWLRPALFAGLG 283

Query: 250 LAIFQQVMGCNTVLYYAPTIFTDVGFGVSAALLAHIGIGIFNVIVTAIAVAIMDKIDRKK 309
           +A F Q+ G   ++YY PT  TD GF  +AAL + +G+    +++T I   ++D + R+K
Sbjct: 284 VAAFTQLSGIEMMIYYTPTFLTDAGFSRAAALHSALGVAAIYLVLTVIGKLLVDHLGRRK 343

Query: 310 IVNIGAVGMGISLFVMSIGMKFSGGSQTAAIISVIALTVYIAFFSATWGPVMWVMIGEVF 369
           +      G  ISL ++ +             + V  L  ++ F S     + W++  EV+
Sbjct: 344 LTLWMMPGAIISLLLLGLVFILDSHGGNHGWLVVSCLFAFMVFNSGGIQVIGWLIGSEVY 403

Query: 370 PLNIRGLGNSFASVINWTANMIVSLTFPSLLDFFGTGSLFIGYGILCFASIWFVQKKVFE 429
           P  IR    S  + + W +N++++ T  SL++  G G     Y +L      F+   V E
Sbjct: 404 PTGIREKATSLHAAMLWGSNLLLTATALSLVNLLGIGGAMWFYALLNLLGFLFIYFVVPE 463

Query: 430 TRNRSLEDIEATLR 443
           T+ RSLE+IE +L+
Sbjct: 464 TKGRSLEEIEISLK 477


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: 588
Number of extensions: 30
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: 457
Length of database: 501
Length adjustment: 34
Effective length of query: 423
Effective length of database: 467
Effective search space:   197541
Effective search space used:   197541
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