Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Dyella79:N515DRAFT_2413 Length = 505 Score = 150 bits (380), Expect = 4e-41 Identities = 79/216 (36%), Positives = 139/216 (64%), Gaps = 3/216 (1%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 +L+ R + K FGA ALDGV + + GEV AL+G NGAGKSTLIK+++G +PDRG + Sbjct: 12 VLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSVEL 71 Query: 64 EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNK--IFLNKKKMMEES 121 +G+ + ++P +A+ GI T+YQ++ L P+L + N++ R + ++ +++ + + Sbjct: 72 DGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQVRDGA 131 Query: 122 KKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVL 181 + LL L + + D++ + + RQ VA+ARA+ SA+++++DEPT++L E R++ Sbjct: 132 RSLLRQLHLEL-DVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRELF 190 Query: 182 ELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRG 217 + L+++G+ +L +TH + Q Y V+DRI VL G Sbjct: 191 RVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDG 226 Score = 80.1 bits (196), Expect = 8e-20 Identities = 53/207 (25%), Positives = 106/207 (51%), Gaps = 4/207 (1%) Query: 12 KSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKVIFN 71 + G L V +++ +GE++ L G G+G++ L +++ G + +RG+L G++V Sbjct: 274 QGLGCRGKLHPVDLQVRRGEMLGLGGLLGSGRTELARLLFGLDRAERGELRIGGERVELK 333 Query: 72 SPNDARSLGIETIYQDL---ALIPDLPIYYNIFLAREVTNKIF-LNKKKMMEESKKLLDS 127 P DA G+ ++ ++ +L + NI LA + +++ + E +++L+ + Sbjct: 334 HPADAVVRGLALCPEERKTDGIVAELSVRENIVLALQARQGWRGMSRARQDELARQLVQA 393 Query: 128 LQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARNL 187 L I+ DI V LSGG +Q V +AR + +++++DEPT + V ++++ Sbjct: 394 LGIKAADIETPVGLLSGGNQQKVMLARWLVTEPRLLILDEPTRGIDVAAKQELMAEVTRR 453 Query: 188 KKKGLGVLIITHNIIQGYEVADRIYVL 214 G+ VL I+ + DRI V+ Sbjct: 454 AHAGMAVLFISAETGELTRWCDRIAVM 480 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: 262 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: 505 Length adjustment: 29 Effective length of query: 222 Effective length of database: 476 Effective search space: 105672 Effective search space used: 105672 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