Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate WP_027721048.1 H589_RS0105145 MFS transporter
Query= SwissProt::P96710 (464 letters) >NCBI__GCF_000425265.1:WP_027721048.1 Length = 469 Score = 267 bits (682), Expect = 6e-76 Identities = 147/457 (32%), Positives = 260/457 (56%), Gaps = 18/457 (3%) Query: 20 MGFVILISCAAGLGGLLYGYDTAVISGAIGFLKDLYSLSPFMEGLVISSIMIGGVVGVGI 79 + FV+L+S AA LGG L+G+DTAVI+GA+ L D + + P + G+ +S ++G VG Sbjct: 14 IAFVLLLSTAAALGGFLFGFDTAVINGAVIALGDYFKVGPVLVGMSVSLALLGSAVGALG 73 Query: 80 SGFLSDRFGRRKILMTAALLFAISAIVSALSQDVSTLIIARIIGGLGIGMGSSLSVTYIT 139 SG++SD++GR K +M AA+LF S + + L V I RI+GG+GIG+ S+++ YI Sbjct: 74 SGYISDKYGRIKGMMLAAVLFTASGVGAGLPFTVWDFIFWRILGGIGIGLASAITPAYIA 133 Query: 140 EAAPPAIRGSLSSLYQLFTILGI-----SATYFINLAVQRSGTYEWGVHTGWRWMLAYGM 194 E +P ++RG SL QL ++GI S + +A +G W WRWM + Sbjct: 134 EISPASLRGRFGSLQQLAIVVGIFIAMLSNYMLVEVAGGSAGNELWFGFETWRWMFWAEV 193 Query: 195 VPSVIFFLVLLVVPESPRWLAKAGKTNEALKILTRINGETVAKEELKNIENSLKIEQMGS 254 P++++ + +++PESPR+L G+ EA +IL ++ G++V E+++ I+ +L++E + Sbjct: 194 PPALLYLIASMMIPESPRYLIGRGRETEAHEILGKVIGDSVL-EKIEEIKVTLQVEGGAA 252 Query: 255 LSQL-FKPGLRKALVIGILLALFNQVIGMNAITYYGPEIFKMMGFGQNAGFVTTCIVGVV 313 + + + G + + +G+ L++ Q +G+N I YYG +++ +GF + T + G+V Sbjct: 253 FADIKGRIGFKHIVWLGLGLSVLQQFVGINVIFYYGSMLWRSVGFTEQHSLWITVVTGIV 312 Query: 314 EVIFTVIAVLLIDKVGRKKLMSIGSAFMAIFMILIGTSFYF---------ELTSGIMMIV 364 ++ T+IA++ ID +GRK L+ GSA M I + ++ F +L Sbjct: 313 NIVTTLIAIVFIDCIGRKPLLLSGSAGMVITLGILAYLFGTAPLDAAGNPKLIGETATTA 372 Query: 365 LILGFVAAFC--VSVGPITWIMISEIFPNHLRARAAGIATIFLWGANWAIGQFVPMMIDS 422 L+ + FC S GP+ W+++ E+F N +RA A + W AN+ + P +++ Sbjct: 373 LVAANIYVFCFGFSWGPVVWVLLGEMFNNRMRASALALGAGAQWVANFVVSASFPSLVEW 432 Query: 423 FGLAYTFWIFAVINILCFLFVVTICPETKNKSLEEIE 459 GL +T+ + + F FV+ + ET+ + LE++E Sbjct: 433 VGLGFTYLGYTFFAAVSFFFVMFLIRETRGRELEDME 469 Lambda K H 0.327 0.142 0.425 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: 584 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: 464 Length of database: 469 Length adjustment: 33 Effective length of query: 431 Effective length of database: 436 Effective search space: 187916 Effective search space used: 187916 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