Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate WP_076479258.1 BW971_RS10475 sugar porter family MFS transporter
Query= SwissProt::P96710 (464 letters) >NCBI__GCF_900156495.1:WP_076479258.1 Length = 495 Score = 291 bits (745), Expect = 3e-83 Identities = 163/459 (35%), Positives = 264/459 (57%), Gaps = 23/459 (5%) Query: 23 VILISCAAGLGGLLYGYDTAVISGAIGFLKDLYSLSPFMEGLVISSIMIGGVVGVGISGF 82 V+ I+ A LGGLL+GYD+AVI+GA+ ++D + ++ G ++S ++G G +G Sbjct: 25 VVRIASVAALGGLLFGYDSAVINGAVSSIQDDFHVADSTLGFAVASALLGAAAGAFSAGR 84 Query: 83 LSDRFGRRKILMTAALLFAISAIVSALSQDVSTLIIARIIGGLGIGMGSSLSVTYITEAA 142 L+DR GR K++ A+LF ISAI +A + ++ TL++ R++GG+G+G+ S ++ YI E + Sbjct: 85 LADRIGRLKVMKIGAVLFFISAIGTAFAPEIWTLVLFRVVGGIGVGVASVIAPAYIAETS 144 Query: 143 PPAIRGSLSSLYQLFTILGISATYFIN-LAVQRSGTYEWGVHTG---WRWMLAYGMVPSV 198 PP +RG L SL QL +LGI + ++ L +G + G WRWM +P+V Sbjct: 145 PPRVRGRLGSLQQLAIVLGIFLSLLVDYLLAHIAGGANEKLALGLDAWRWMFLAMAIPAV 204 Query: 199 IFFLVLLVVPESPRWLAKAGKTNEALKILTRINGETVAKEELKNIENSLKIEQMGSLSQL 258 ++ L+ +PESPR+L + EA ++LT + GE + + I++SL + S L Sbjct: 205 VYGLLASTIPESPRYLVATQRLPEARRVLTLLFGEKNLELTITRIQDSLAGDTKPSWKDL 264 Query: 259 FKP---GLRKALVIGILLALFNQVIGMNAITYYGPEIFKMMGFGQNAGFVTTCIVGVVEV 315 +P G+ + +G+LL++F Q +G+N I YY +++ +GF +N F T+ +V + Sbjct: 265 ARPGGGGIYPIVWVGLLLSVFQQAVGINVIFYYSNILWEAVGFKENQAFQTSVFTSLVNI 324 Query: 316 IFTVIAVLLIDKVGRKKLMSIGSAFMAIFM----ILIGTSFYFELTSGIM---------M 362 + T +A+ L+DK+GRK L+ IGSA MA+ + I GT+ G+M Sbjct: 325 VATFVAIALVDKIGRKPLLLIGSAGMAVTLGVMAICFGTAAQQPNADGVMEPHLTGAAGP 384 Query: 363 IVLILG--FVAAFCVSVGPITWIMISEIFPNHLRARAAGIATIFLWGANWAIGQFVPMMI 420 I LI FV F +S GP+ W+++ EIFPN +R A +A W ANWAI P + Sbjct: 385 IALIAANLFVVFFALSWGPVVWVLLGEIFPNRIRGAALSLAAAGQWAANWAITVSFP-SL 443 Query: 421 DSFGLAYTFWIFAVINILCFLFVVTICPETKNKSLEEIE 459 SF L + + ++A+ +L LFV ETK SLE+++ Sbjct: 444 KSFSLGFAYGMYALFAVLSLLFVARFVRETKGMSLEDMD 482 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: 507 Number of extensions: 27 Number of successful extensions: 6 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: 495 Length adjustment: 34 Effective length of query: 430 Effective length of database: 461 Effective search space: 198230 Effective search space used: 198230 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