Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate N515DRAFT_1228 N515DRAFT_1228 MFS transporter, SP family, galactose:H+ symporter
Query= SwissProt::P0AE24 (472 letters) >FitnessBrowser__Dyella79:N515DRAFT_1228 Length = 463 Score = 504 bits (1299), Expect = e-147 Identities = 265/468 (56%), Positives = 336/468 (71%), Gaps = 6/468 (1%) Query: 4 INTESALTPRSLRDTRRMNMFVSVAAAVAGLLFGLDIGVIAGALPFITDHFVLTSRLQEW 63 +N+++ TP + + ++ V AA+AGL+FGLDIGVI+GA FI F ++ EW Sbjct: 1 MNSQAIATPTA--HVKGTVIYTCVLAALAGLMFGLDIGVISGASQFIKAEFAISDHTIEW 58 Query: 64 VVSSMMLGAAIGALFNGWLSFRLGRKYSLMAGAILFVLGSIGSAFATSVEMLIAARVVLG 123 +VSSMM GAA+GAL GWLS LGRK SL+ GAILFV+GS+ A S E LIAARV+LG Sbjct: 59 IVSSMMFGAAVGALGAGWLSSHLGRKRSLILGAILFVIGSLLCGLAWSPETLIAARVILG 118 Query: 124 IAVGIASYTAPLYLSEMASENVRGKMISMYQLMVTLGIVLAFLSDTAFSYSGNWRAMLGV 183 +A+GIA++TAPLYL+E+A E++RG MIS YQLM+T+GI++AFLSDTA SY G WR MLGV Sbjct: 119 LAIGIATFTAPLYLAEVAPEHIRGAMISTYQLMITIGILVAFLSDTALSYHGAWRWMLGV 178 Query: 184 LALPAVLLIILVVFLPNSPRWLAEKGRHIEAEEVLRMLRDTSEKAREELNEIRESLKLKQ 243 +A+P L ++ V+ LP+SPRWL +GR EA +VLR LR E +I E LK Q Sbjct: 179 IAIPGALFLLGVLGLPDSPRWLMMRGRRDEAIDVLRRLRGDEVVVAREAADIEEQLKTPQ 238 Query: 244 GGWALFKINRNVRRAVFLGMLLQAMQQFTGMNIIMYYAPRIFKMAGFTTTEQQMIATLVV 303 GW LF N N RR+VFLG LLQ MQQFTGMN++MYYAPRIF+ G+ T QM T +V Sbjct: 239 RGWDLFAENPNFRRSVFLGALLQIMQQFTGMNVVMYYAPRIFQEMGYDTA-AQMWFTALV 297 Query: 304 GLTFMFATFIAVFTVDKAGRKPALKIGFSVMALGTLVLGYCLMQFDNGTASSGLSWLSVG 363 GLT + ATFIA+ +D+ GRKP L GF+VMA+G V+G + NG + V Sbjct: 298 GLTNVLATFIAIALIDRWGRKPILYTGFAVMAVGLGVVGALMNGGINGQTE---QYTCVA 354 Query: 364 MTMMCIAGYAMSAAPVVWILCSEIQPLKCRDFGITCSTTTNWVSNMIIGATFLTLLDSIG 423 M + I G+AMSA P+VW LCSEIQPLK RDFGI ST TNW++NM++G TFL+LL++IG Sbjct: 355 MLLFFIVGFAMSAGPLVWTLCSEIQPLKGRDFGIGVSTFTNWITNMVVGFTFLSLLNTIG 414 Query: 424 AAGTFWLYTALNIAFVGITFWLIPETKNVTLEHIERKLMAGEKLRNIG 471 A TFWLY ALN F+ +TFWL+PETK VTLE IER LMAG++LR+IG Sbjct: 415 NASTFWLYAALNAVFIVLTFWLVPETKGVTLEQIERNLMAGKRLRDIG 462 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: 778 Number of extensions: 42 Number of successful extensions: 4 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: 463 Length adjustment: 33 Effective length of query: 439 Effective length of database: 430 Effective search space: 188770 Effective search space used: 188770 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 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