Align Galactose-proton symporter; Galactose transporter (characterized)
to candidate N515DRAFT_1228 N515DRAFT_1228 MFS transporter, SP family, galactose:H+ symporter
Query= SwissProt::P0AEP1 (464 letters) >FitnessBrowser__Dyella79:N515DRAFT_1228 Length = 463 Score = 605 bits (1559), Expect = e-177 Identities = 302/450 (67%), Positives = 356/450 (79%), Gaps = 1/450 (0%) Query: 12 KAMTFFVCFLAALAGLLFGLDIGVIAGALPFIADEFQITSHTQEWVVSSMMFGAAVGAVG 71 K + C LAALAGL+FGLDIGVI+GA FI EF I+ HT EW+VSSMMFGAAVGA+G Sbjct: 14 KGTVIYTCVLAALAGLMFGLDIGVISGASQFIKAEFAISDHTIEWIVSSMMFGAAVGALG 73 Query: 72 SGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLGLAVGVASYTAPLYLS 131 +GWLS LGRK+SL++GAILFV GSL A + E LI +RV+LGLA+G+A++TAPLYL+ Sbjct: 74 AGWLSSHLGRKRSLILGAILFVIGSLLCGLAWSPETLIAARVILGLAIGIATFTAPLYLA 133 Query: 132 EIAPEKIRGSMISMYQLMITIGILGAYLSDTAFSYTGAWRWMLGVIIIPAILLLIGVFFL 191 E+APE IRG+MIS YQLMITIGIL A+LSDTA SY GAWRWMLGVI IP L L+GV L Sbjct: 134 EVAPEHIRGAMISTYQLMITIGILVAFLSDTALSYHGAWRWMLGVIAIPGALFLLGVLGL 193 Query: 192 PDSPRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESLQVKQSGWALFKENSNFRRA 251 PDSPRW + R +A VL RLR RE +I E L+ Q GW LF EN NFRR+ Sbjct: 194 PDSPRWLMMRGRRDEAIDVLRRLRGDEVVVAREAADIEEQLKTPQRGWDLFAENPNFRRS 253 Query: 252 VFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYTNTTEQMWGTVIVGLTNVLATFIAIGLV 311 VFLG LLQ+MQQFTGMNV+MYYAP+IF+ GY +T QMW T +VGLTNVLATFIAI L+ Sbjct: 254 VFLGALLQIMQQFTGMNVVMYYAPRIFQEMGY-DTAAQMWFTALVGLTNVLATFIAIALI 312 Query: 312 DRWGRKPTLTLGFLVMAAGMGVLGTMMHIGIHSPSAQYFAIAMLLMFIVGFAMSAGPLIW 371 DRWGRKP L GF VMA G+GV+G +M+ GI+ + QY +AMLL FIVGFAMSAGPL+W Sbjct: 313 DRWGRKPILYTGFAVMAVGLGVVGALMNGGINGQTEQYTCVAMLLFFIVGFAMSAGPLVW 372 Query: 372 VLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNTLGNANTFWVYAALNVLFILL 431 LCSEIQPLKGRDFGI ST TNWI NM+VG TFL++LNT+GNA+TFW+YAALN +FI+L Sbjct: 373 TLCSEIQPLKGRDFGIGVSTFTNWITNMVVGFTFLSLLNTIGNASTFWLYAALNAVFIVL 432 Query: 432 TLWLVPETKHVSLEHIERNLMKGRKLREIG 461 T WLVPETK V+LE IERNLM G++LR+IG Sbjct: 433 TFWLVPETKGVTLEQIERNLMAGKRLRDIG 462 Lambda K H 0.327 0.140 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: 867 Number of extensions: 37 Number of successful extensions: 2 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: 463 Length adjustment: 33 Effective length of query: 431 Effective length of database: 430 Effective search space: 185330 Effective search space used: 185330 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