Align Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized)
to candidate WP_008347408.1 BA79_RS16380 amino acid permease
Query= TCDB::P24207 (458 letters) >NCBI__GCF_000691145.1:WP_008347408.1 Length = 448 Score = 372 bits (956), Expect = e-107 Identities = 178/442 (40%), Positives = 279/442 (63%), Gaps = 3/442 (0%) Query: 19 LHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYGVAGIIAFLIMRQLGEMV 78 L R L NRH+QLIA+GG IGTGLFLG G AIQ+AGP+++ Y + G+ F +MR LGE++ Sbjct: 6 LKRDLSNRHVQLIAIGGTIGTGLFLGSGKAIQLAGPSIIFAYLIVGMAIFFVMRALGELL 65 Query: 79 VEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYWFPDVPTWIW 138 + + S A Y GP+A F++GW YW +++ MA++ A G+Y+QYWF D+P WI Sbjct: 66 LSKAGYQSLTDIAEDYLGPWASFVTGWTYWFCWIMTAMADVIAVGVYVQYWF-DIPQWIP 124 Query: 139 AAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMIGFGLWLLFSGHGGEKA--SIDN 196 A +I+ NL+ V+L+GE EFWFALIKV+ I+ +IG G+ LL G + ++ N Sbjct: 125 AIICLLILLGFNLLTVKLFGEMEFWFALIKVITILLLIGVGIVLLIIGFQTDAGPVTVTN 184 Query: 197 LWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSIPKAVNQVVYRILLF 256 LW +GG F G G +LS +++F++ G+EL+G++AAE +P+K+IP A+N++ RIL F Sbjct: 185 LWSHGGLFPNGVTGFLLSFQMVIFAYVGVELVGVSAAETANPQKNIPSAINKIPLRILFF 244 Query: 257 YIGSLVVLLALYPWVEVKSNSSPFVMIFHNLDSNVVASALNFVILVASLSVYNSGVYSNS 316 Y+G++ VLL + PW E+ ++ SPFV F + V A +NFV+L ++ S NSG++S S Sbjct: 245 YVGAIFVLLCINPWTELSASESPFVKTFGLIGIPVAAGLINFVVLTSAASACNSGMFSTS 304 Query: 317 RMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAITSLVVLINYLLPQKAFGLLMALVVA 376 R+L+ LS Q P R+++ VP N+L +S + S+ L++ L+P++AFG++ + Sbjct: 305 RILYNLSHQKQGPASFGRLNKHAVPSNALFVSTIVVSVGALLSKLIPEQAFGIVTTISAI 364 Query: 377 TLLLNWIMICLAHLRFRAAMRRQGRETQFKALLYPFGNYLCIAFLGMILLLMCTMDDMRL 436 + W +I + HL+++ + + FKA PF N + IL++M D R Sbjct: 365 CFIWVWSIILICHLKYKKTRPELHKASTFKAPFTPFVNIAVLVLFAAILVIMLFADATRP 424 Query: 437 SAILLPVWIVFLFMAFKTLRRK 458 + +L PVW FLF+ + +R+ Sbjct: 425 ALLLTPVWFGFLFLIYARKKRR 446 Lambda K H 0.329 0.143 0.447 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: 581 Number of extensions: 24 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: 458 Length of database: 448 Length adjustment: 33 Effective length of query: 425 Effective length of database: 415 Effective search space: 176375 Effective search space used: 176375 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 (21.8 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