Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate WP_012411593.1 NPUN_RS26935 MFS transporter
Query= SwissProt::P96710 (464 letters) >NCBI__GCF_000020025.1:WP_012411593.1 Length = 466 Score = 268 bits (686), Expect = 2e-76 Identities = 162/466 (34%), Positives = 253/466 (54%), Gaps = 26/466 (5%) Query: 14 VTRSHSMGFVILISCAAGLGGLLYGYDTAVISGAIGFLKDLYSLSPFMEGLVISSIMIGG 73 V R + +VILI+ AA LGG L+G+DTAVI+GA+ L ++ S ++ GL +S ++G Sbjct: 6 VRRKSNTFYVILIAGAAALGGFLFGFDTAVINGAVLSLAKAFNTSSWVTGLAVSLALLGS 65 Query: 74 VVGVGISGFLSDRFGRRKILMTAALLFAISAIVSALSQDVSTLIIARIIGGLGIGMGSSL 133 VG +G ++DR+GR K ++ A++LF ISAI S ++ + I R++GG+GIG+ S + Sbjct: 66 AVGAFFAGQIADRYGRVKAMVVASVLFTISAIGSGMAFTIWDFIFWRVLGGIGIGVASVI 125 Query: 134 SVTYITEAAPPAIRGSLSSLYQLFTILGI----SATYFI-NLAVQRSGTYEWGVHTGWRW 188 + YI E +P +RG L SL QL ++GI + YFI A + +GV WRW Sbjct: 126 APAYIAECSPTHLRGRLGSLQQLAIVVGIFVALLSDYFIATSAGSADSPFLFGV-AAWRW 184 Query: 189 MLAYGMVPSVIFFLVLLVVPESPRWLAKAGKTNEALKILTRINGETVAKEELKNIENSLK 248 M + P+V + +V L +PESPR+L G+ +EA+ +LT+I G V +++ I ++ Sbjct: 185 MFWTAVPPAVFYGMVALTIPESPRYLVAKGRESEAVNVLTKILGGDVL-PKIEEIRQTVL 243 Query: 249 IEQMGSLSQLF--KPGLRKALVIGILLALFNQVIGMNAITYYGPEIFKMMGFGQNAGFVT 306 E+ S L GL + IGI L++ Q +G+N I YY +++ +GF + Sbjct: 244 RERQPKFSDLLSRSGGLLPIVWIGIGLSVLQQFVGINVIFYYSSVLWRAVGFSEKDSLSI 303 Query: 307 TCIVGVVEVIFTVIAVLLIDKVGRKKLMSIGSAFMAIFMILIGTSFYF------------ 354 T I G V +I T+IA+ +DK GRK L+ IGS M + +GT Y Sbjct: 304 TVITGAVNIITTLIAIAFVDKFGRKPLLIIGSIGMT---LTLGTMAYIFGNAPLDAAGNP 360 Query: 355 ELTSGIMMIVLILGFVAAFC--VSVGPITWIMISEIFPNHLRARAAGIATIFLWGANWAI 412 L + LI + FC S GPI W+++ E+F N +RA A +A W AN+ I Sbjct: 361 SLAGSAGTVALIAANLYVFCFGFSWGPIVWVLLGEMFNNKIRAAALSVAAAIQWVANFLI 420 Query: 413 GQFVPMMIDSFGLAYTFWIFAVINILCFLFVVTICPETKNKSLEEI 458 P ++ FGL + ++ + F F++ ETK LE++ Sbjct: 421 STTFPPILQYFGLGSAYGLYTIAAATSFFFILFFIKETKGIELEDM 466 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: 547 Number of extensions: 28 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: 466 Length adjustment: 33 Effective length of query: 431 Effective length of database: 433 Effective search space: 186623 Effective search space used: 186623 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