Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >NCBI__GCF_002019605.1:WP_078427103.1 Length = 509 Score = 148 bits (373), Expect = 2e-40 Identities = 76/237 (32%), Positives = 142/237 (59%), Gaps = 1/237 (0%) Query: 1 MSDLLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGD 60 MS ++E++D+ K F + A D V++++ +GE+ ALLG+NGAGKSTL+ ++ G ++P++G+ Sbjct: 1 MSYVIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGE 60 Query: 61 LVFEGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEE 120 ++ +GK V PN A LGI ++Q L+ + NI L +E T +N KK + Sbjct: 61 ILVKGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKINIKKAAKA 120 Query: 121 SKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKV 180 + + + + D K++++S G +Q V + + +Y A++++ DEPTAAL+ E ++ Sbjct: 121 VETISKQYGLAV-DPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITEL 179 Query: 181 LELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVM 237 +++ + L +G +++ITH + + EV DR V+ RG+ I E+ + + +M Sbjct: 180 IQIMKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMM 236 Score = 95.1 bits (235), Expect = 2e-24 Identities = 65/242 (26%), Positives = 122/242 (50%), Gaps = 8/242 (3%) Query: 4 LLEIRD-VHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLV 62 +L+I+D V K + A++ + +E++ GE++ + G +G G++ LI+ I+G KP G++ Sbjct: 256 VLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIEAITGLRKPTGGNIQ 315 Query: 63 FEGKKVIFNSPNDARSLGIETIYQDL---ALIPDLPIYYNIFLA----REVTNKIFLNKK 115 G+ + +P G+ I QD L+ D + NI L + + LN Sbjct: 316 LNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQTYYQKPYSTSGVLNFN 375 Query: 116 KMMEESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVV 175 ++ +++ +L++ +R P + LSGG +Q +AR V S +++ +PT L V Sbjct: 376 EIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSPDLLIAAQPTRGLDVG 435 Query: 176 EARKVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITE 235 + + KG VL+I+ + + V+DRI V+ GKI+ ++TN E+ Sbjct: 436 AIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVAIVDADKTNENELGL 495 Query: 236 VM 237 +M Sbjct: 496 LM 497 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: 323 Number of extensions: 12 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: 509 Length adjustment: 29 Effective length of query: 222 Effective length of database: 480 Effective search space: 106560 Effective search space used: 106560 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 Apr 09 2024. 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