Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate WP_034992666.1 DL88_RS04730 sugar porter family MFS transporter
Query= SwissProt::P0AE24 (472 letters) >NCBI__GCF_000745425.1:WP_034992666.1 Length = 489 Score = 241 bits (614), Expect = 5e-68 Identities = 147/446 (32%), Positives = 238/446 (53%), Gaps = 11/446 (2%) Query: 21 MNMFVSVAAAVAGLLFGLDIGVIAGALPFITDHFVLTSRLQEWVVSSMMLGAAIGALFNG 80 M + AA+ G L+G D G+I+GAL IT F L S +QE V ++++ GA +GAL G Sbjct: 32 MLALAATVAAICGGLYGYDTGIISGALILITREFQLPSNMQEIVAAAILAGAVVGALATG 91 Query: 81 WLSFRLGRKYSLMAGAILFVLGSIGSAFATSVEMLIAARVVLGIAVGIASYTAPLYLSEM 140 LS +GR+ S++ I++++G++ A A SV L+AAR LG+AVG ++ P+Y+SE+ Sbjct: 92 SLSEAIGRRRSVIVVTIVYMIGAVACALAPSVWSLVAARFFLGLAVGGSTQVVPMYISEL 151 Query: 141 ASENVRGKMISMYQLMVTLGIVLAFLSDTAFSYSGNWRAMLGVLALPAVLLIILVVFLPN 200 A + RGK+++++ + + +GI+LA + WR M+ + A+PA ++ + + FLP Sbjct: 152 APSDRRGKLVTLFNVAIGIGILLANIVGFTLHEVWTWREMVAIAAIPAFIVFVSMFFLPQ 211 Query: 201 SPRWLAEKGRHIEAEEVLRMLRDTSEKAREELN---EIRESLKLKQGGWALFKINRNVRR 257 SPRW AE A E LR +R+ +E+N E+ E + + GW VR Sbjct: 212 SPRWAAENIGLHGALESLRRVRNCHRTIHKEVNQIQEVAERTRDEDRGWRGLS-QPWVRP 270 Query: 258 AVFLGMLLQAMQQFTGMNIIMYYAPRIFKMAGFTTTEQQMIATLVVGLTFMFATFIAVFT 317 A+ + + Q G+ +++YYAP AGF + ++A+L V + + T I Sbjct: 271 ALVAALGVAVFTQCGGLEMMIYYAPTFLSQAGFGAS-SALLASLGVAIVYCVMTLIGCLN 329 Query: 318 VDKAGRKPALKI--GFSVMALGTLVLGYCLMQFDNGTASSGLSWLSVGMTMMCIAGYAMS 375 VD+ GR+ + I SV++L L + + + G A SWL + ++ I A Sbjct: 330 VDRIGRRRLMLIMCPGSVLSLIGLGIVFAMHPAPGGFA----SWLVIAFLLLFIMFNAGG 385 Query: 376 AAPVVWILCSEIQPLKCRDFGITCSTTTNWVSNMIIGATFLTLLDSIGAAGTFWLYTALN 435 V W+L +E+ PL R + T W SN+I+ T L+L+ +G GT W Y +N Sbjct: 386 IQVVGWLLGAEMFPLSMRSQATSLHAATLWGSNLIVTGTALSLVHLLGLGGTMWFYAGVN 445 Query: 436 IAFVGITFWLIPETKNVTLEHIERKL 461 +A + +PET +LE IE L Sbjct: 446 VASFLFVLFFVPETAGSSLEDIEAAL 471 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: 555 Number of extensions: 29 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: 489 Length adjustment: 34 Effective length of query: 438 Effective length of database: 455 Effective search space: 199290 Effective search space used: 199290 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