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.
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:
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