Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate BWI76_RS07360 BWI76_RS07360 phenylalanine transporter
Query= TCDB::P40812 (497 letters) >FitnessBrowser__Koxy:BWI76_RS07360 Length = 458 Score = 330 bits (845), Expect = 8e-95 Identities = 174/439 (39%), Positives = 272/439 (61%), Gaps = 21/439 (4%) Query: 27 HKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRALGELVL 86 H+ + NR +Q+IA+GGAIGTGLFLG G +QMAGPA+ L Y + GI +F I+R LGE+V+ Sbjct: 19 HRGLQNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYAVAGIVAFLIMRQLGEMVV 78 Query: 87 HRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGDVPQWV 146 P SGSF +A ++ G A +++GW Y++ + + G+ ++TA +YM YW DVP W+ Sbjct: 79 EEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYW--LPDVPTWI 136 Query: 147 FALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIFLGTGQPLEGNATGFH 206 +A I+ +N++ V+ + E EFWFALIKVLAI+ + G L G G+ G Sbjct: 137 WAAAFFLIINAVNLVNVRLYGEAEFWFALIKVLAIIGMIGFGLWMLFGGHG--GSKAGID 194 Query: 207 LITDNGGFFP---HGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINSVIWR 263 + +GGFF HGL+ +L +I +F+F +EL+G A E ++P+K +PKA+N V++R Sbjct: 195 NLWKHGGFFATGWHGLIMSLAVI---MFSFGGLELIGITAAEAQNPEKSIPKAVNQVVYR 251 Query: 264 IGLFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSLNSGL 323 I LFY+GS+V+L+ L PW Q+ SPFV F L + S +N V+L A+LS NSG+ Sbjct: 252 ILLFYIGSLVVLLALYPWVEIQSDSSPFVMIFHNLDSNVVASALNFVILVASLSVYNSGV 311 Query: 324 YCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFEIVLN 383 Y R+L +S+ G+APKF+A++S++ VP +L + ++ + V LNYL+P + +++ Sbjct: 312 YSNSRMLFGLSVQGNAPKFLARVSKRGVPVNSLLLSGIITSLVVVLNYLLPQKALGLLMA 371 Query: 384 FASLGIIASWAFIMVCQMRLR-QAIKEGKAADVSFKLPGAPFTSWLTLLFLLSVLVLMAF 442 ++ +W IM+C L+ +A + K + FK +P ++++ + FL +LVLM Sbjct: 372 LVVATLLLNW--IMICLAHLKFRAAQRRKGREPKFKALLSPASNYICIAFLALILVLMC- 428 Query: 443 DYPNGTYTIASLPLIAILL 461 TI + L AILL Sbjct: 429 -------TIDGMRLSAILL 440 Lambda K H 0.328 0.140 0.434 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: 633 Number of extensions: 40 Number of successful extensions: 3 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: 497 Length of database: 458 Length adjustment: 33 Effective length of query: 464 Effective length of database: 425 Effective search space: 197200 Effective search space used: 197200 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