Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate WP_012112843.1 XAUT_RS04125 MFS transporter
Query= SwissProt::P0AE24 (472 letters) >NCBI__GCF_000017645.1:WP_012112843.1 Length = 456 Score = 286 bits (732), Expect = 1e-81 Identities = 164/458 (35%), Positives = 265/458 (57%), Gaps = 16/458 (3%) Query: 21 MNMFVSVAAAVAGLLFGLDIGVIAGALPFITDHFVLTSRLQEWVVSSMMLGAAIGALFNG 80 M ++ A +AG LFG D GVIAGAL + + + + +++ GA +GA+ G Sbjct: 1 MMYLIAAIAGIAGALFGFDEGVIAGALAPLRRDLGIDPVAEGMMTAAVPFGAFLGAIVGG 60 Query: 81 WLSFRLGRKYSLMAGAILFVLGSIGSAFATSVEMLIAARVVLGIAVGIASYTAPLYLSEM 140 L+ LGR+ L+A A+LFV+G++ SAFA + L AR+++G+ VG+A+ APLY+SE Sbjct: 61 RLALALGRRRLLLAAAVLFVVGALLSAFAFGLWTLTFARLIIGLGVGVAAMMAPLYISEC 120 Query: 141 ASENVRGKMISMYQLMVTLGIVLAFLSDTAFSYSGNWRAMLGVLALPAVLLIILVVFLPN 200 A RG ++S+YQL +TLGI+ A++ AF S WR M V A+PA+ L + + L + Sbjct: 121 APAAQRGMLVSIYQLAITLGILGAYVVGYAFHES--WRWMFAVGAVPAIALFVGIFGLSD 178 Query: 201 SPRWLAEKGRHIEAEEVLRMLRDTSEK---AREELNEIRESLKLKQGGWALFK--INRNV 255 +PRWLA +GR EA L +R+ SE + E EI + A + V Sbjct: 179 TPRWLAVRGREAEARAALARVREKSESDPAVKAEFAEILTGATQDENRKARLSDLLTPRV 238 Query: 256 RRAVFLGMLLQAMQQFTGMNIIMYYAPRIFKMAGFTTTEQQMIATLVVGLTFMFATFIAV 315 R A+ + M L +QQ +G+N ++YYAP +F+++GF++T Q++AT +G+ + T + + Sbjct: 239 RPALIVAMGLFLLQQLSGINAVIYYAPTVFELSGFSSTTTQILATAGIGVVNVLMTLVGM 298 Query: 316 FTVDKAGRKPALKIGF--SVMALGTLVLGYCLMQFDNGTASSGLSWLSVGMTMMCIAGYA 373 +D+ GR+ L IGF + +AL + +G T S + L++G ++ IA +A Sbjct: 299 ALIDRLGRRLLLLIGFAGTAVALSVIAIG-------AATGSEMMGKLALGGLVLYIASFA 351 Query: 374 MSAAPVVWILCSEIQPLKCRDFGITCSTTTNWVSNMIIGATFLTLLDSIGAAGTFWLYTA 433 ++ P+ W++ SE+ PL R G++ ++ NW N ++ +F L+ G AG F LY Sbjct: 352 IAIGPLPWVMMSEVFPLDVRALGMSIASLVNWGFNFLVVFSFPVLVAEFGLAGVFGLYAV 411 Query: 434 LNIAFVGITFWLIPETKNVTLEHIERKLMAGEKLRNIG 471 + + + T WL+PET V+LE IER L +G LR++G Sbjct: 412 VCVVGLAFTQWLVPETSGVSLEEIERHLDSGRPLRDLG 449 Lambda K H 0.327 0.138 0.409 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: 620 Number of extensions: 33 Number of successful extensions: 5 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: 472 Length of database: 456 Length adjustment: 33 Effective length of query: 439 Effective length of database: 423 Effective search space: 185697 Effective search space used: 185697 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