Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate H281DRAFT_04149 H281DRAFT_04149 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Burk376:H281DRAFT_04149 Length = 506 Score = 168 bits (425), Expect = 2e-46 Identities = 88/238 (36%), Positives = 154/238 (64%), Gaps = 2/238 (0%) Query: 1 MSDLLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGD 60 M +L++ ++ KSF VKAL G+ +EI +GE+ ALLG+NGAGKSTL+KI+ G ++PD G Sbjct: 1 MDTILKLDNITKSFPGVKALQGIHLEIARGEIHALLGENGAGKSTLMKILCGIYQPDEGT 60 Query: 61 LVFEGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKI-FLNKKKMME 119 + EG+ F + +DA + G+ ++Q+ +LIP L N+FL RE+ N + LN+ M Sbjct: 61 ITIEGEPRHFANYHDAVAAGVGIVFQEFSLIPYLNAVENMFLGREMKNGLGLLNRGGMRR 120 Query: 120 ESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARK 179 + ++ L + I D+++ + LS Q+Q V + +A+ A+++++DEPTA L+ EA Sbjct: 121 VAAEIFGRLGVSI-DLSVPIRELSVAQQQFVEIGKALSLEARILILDEPTATLTPAEAEH 179 Query: 180 VLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVM 237 + + R+LKK+G+ ++ I+H++ + +EV DRI VL G+ + + +++V + E+M Sbjct: 180 LFAIMRDLKKQGVAMIFISHHLEEIFEVCDRITVLRDGQYVGMTEVAQSDVGRLVEMM 237 Score = 70.5 bits (171), Expect = 6e-17 Identities = 44/199 (22%), Positives = 95/199 (47%), Gaps = 6/199 (3%) Query: 27 INKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKVIFNSPNDARSLGIETIYQ 86 + +GE++ G G+G++ + G ++ G+ + P DA G+ + + Sbjct: 278 LREGEILGFAGLVGSGRTETALAVIGADPAHVKEIRINGEAANLSDPADALRAGVGILPE 337 Query: 87 DL---ALIPDLPIYYNIF---LAREVTNKIFLNKKKMMEESKKLLDSLQIRIPDINMKVE 140 LI D I NI L + + + F++++ + ++ + ++ P ++ +V Sbjct: 338 SRKTEGLITDFSIKQNISINNLGKYRSLRFFIDQRSEARATADIMKRVGVKAPTMHTEVA 397 Query: 141 NLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARNLKKKGLGVLIITHN 200 LSGG +Q V +AR + +++ DEPT + V ++ L R L +G +++I+ Sbjct: 398 TLSGGNQQKVVIARWLNHHTNILIFDEPTRGIDVGAKAEIYLLMRELTARGYSIIMISSE 457 Query: 201 IIQGYEVADRIYVLDRGKI 219 + + + DR+ V +G+I Sbjct: 458 LPEIVGMCDRVAVFRQGRI 476 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: 270 Number of extensions: 9 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: 506 Length adjustment: 29 Effective length of query: 222 Effective length of database: 477 Effective search space: 105894 Effective search space used: 105894 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