Align sugar transport protein 13 (characterized)
to candidate WP_084936573.1 HA51_RS21365 sugar porter family MFS transporter
Query= CharProtDB::CH_091463 (526 letters) >NCBI__GCF_002095475.1:WP_084936573.1 Length = 464 Score = 214 bits (544), Expect = 7e-60 Identities = 145/469 (30%), Positives = 238/469 (50%), Gaps = 41/469 (8%) Query: 22 IVIISCIMAATGGLMFGYDVGVSGGVTSMPDFLEKFFPVVYRKVVAGADKDSNYCKYDNQ 81 + + C +AA GL+FG D+GV G ++P F+ K F V + Sbjct: 15 MTLFVCFLAALAGLLFGLDIGVIAG--ALP-FIAKDFNVTAHQQ---------------- 55 Query: 82 GLQLFTSSLYLAGLTATFFASYTTRTLGRRLTMLIAGVFFIIGVALNAGAQDLAMLIAGR 141 + SS+ + + + LGR+ +++ + F+IG +A A MLIA R Sbjct: 56 --EWIVSSMMFGAAVGAVGSGWMSSRLGRKKSLMAGAILFVIGSLWSAMATSPDMLIAAR 113 Query: 142 ILLGCGVGFANQAVPLFLSEIAPTRIRGGLNILFQLNVTIGILFANLVNYGTAKIKGGWG 201 ++LG VG A+ PL+LSEIAP +IRG + L+QL +TIGIL A L + TA G Sbjct: 114 VVLGLAVGVASYTAPLYLSEIAPEKIRGSMISLYQLMITIGILAAYLSD--TAFSDAG-A 170 Query: 202 WRLSLGLAGIPALLLTVGALLVTETPNSLVERGRLDEGKAVLRRIRGT-DNVEPEFADLL 260 WR LG+ IPA+LL +G + +P L +G + VL R+R T + + E ++ Sbjct: 171 WRWMLGVITIPAILLLIGVFFLPNSPRWLAAKGDFRSAQRVLDRLRDTSEQAKRELDEIR 230 Query: 261 EASRLAKEVKHPFRNLLQRRNRPQLVIAVALQIFQQCTGINAIMFYAPVLFSTLGFGSDA 320 E+ ++ + F++ R + + V LQ+ QQ TG+N IM+YAP +F GF + Sbjct: 231 ESLKIKQSGWQLFQS--NSHFRRAVYLGVLLQVMQQFTGMNVIMYYAPKIFEIAGFANTT 288 Query: 321 -SLYSAVVTGAVNVLSTLVSIYSVDKVGRRVLLLEAGVQMFFSQVVIAIILGVKVTDTST 379 ++ V+ G VNVL+T ++I VD+ GR+ L+ + M ++ +L + + S Sbjct: 289 QQMWGTVIVGLVNVLATFIAIGLVDRWGRKPTLVLGFIVMAAGMGILGTMLHIGIHSASA 348 Query: 380 NLSKGFAILVVVMICTYVAAFAWSWGPLGWLIPSETFPLETRSAGQSVTVCVNLLFTFII 439 V M+ ++ FA S GPL W++ SE PL+ R G +V+ N + I+ Sbjct: 349 Q------YFAVAMLLMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITVSTATNWIANMIV 402 Query: 440 AQAFLSMLCHF----KFGIFIFFSAWVLIMSVFVMFLLPETKNIPIEEM 484 FL+ML F ++ + + ++++V L+PETKN+ +E + Sbjct: 403 GATFLTMLNSLGNAPTFWVYAGLNVFFILLTV---ALIPETKNVSLEHI 448 Lambda K H 0.326 0.141 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: 600 Number of extensions: 33 Number of successful extensions: 7 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: 526 Length of database: 464 Length adjustment: 34 Effective length of query: 492 Effective length of database: 430 Effective search space: 211560 Effective search space used: 211560 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: 52 (24.6 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