Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate 7024900 Shewana3_2074 ABC transporter related (RefSeq)
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__ANA3:7024900 Length = 499 Score = 173 bits (439), Expect = 5e-48 Identities = 92/242 (38%), Positives = 151/242 (62%), Gaps = 1/242 (0%) Query: 1 MSDLLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGD 60 MS +LE++ + K + VKAL+ VS+ + GEV ALLG+NGAGKSTL+K+++G D GD Sbjct: 1 MSLILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGD 60 Query: 61 LVFEGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEE 120 ++F G+ FN+P DA+ GI T+YQ++ L+P+L + N+FL E ++ KKM + Sbjct: 61 ILFLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYAD 120 Query: 121 SKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKV 180 ++ +L ++ I D++ + + S +Q +A+AR V SAK++++DEPTA+L E + + Sbjct: 121 ARAVLTQFKLDI-DVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVL 179 Query: 181 LELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTSF 240 + LK KG+ ++ ITH + Q Y+++DRI VL G+ I E ++ E M Sbjct: 180 FGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGR 239 Query: 241 AL 242 +L Sbjct: 240 SL 241 Score = 89.7 bits (221), Expect = 1e-22 Identities = 61/217 (28%), Positives = 113/217 (52%), Gaps = 11/217 (5%) Query: 4 LLEIRDVHKSFGAVK-ALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLV 62 LL + DV +VK ++ +++ + KG+ V L G G+G+S + + G D G + Sbjct: 262 LLSLEDV-----SVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIH 316 Query: 63 FEGKKVIFNSPNDARSLGIETIYQDL---ALIPDLPIYYNIFLAREVTNKI--FLNKKKM 117 G+K+ + P DA S GI +D +I L I NI LA + +L+ + Sbjct: 317 LAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQARIGWWRYLSNTRQ 376 Query: 118 MEESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEA 177 E ++ +D LQI PD + +E LSGG +Q V +AR + ++++DEPT + + Sbjct: 377 QEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAH 436 Query: 178 RKVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVL 214 ++++L R L +G+ +L+ + + + ++++ VL Sbjct: 437 AEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVL 473 Lambda K H 0.318 0.137 0.371 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: 244 Number of extensions: 14 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 251 Length of database: 499 Length adjustment: 29 Effective length of query: 222 Effective length of database: 470 Effective search space: 104340 Effective search space used: 104340 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: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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