Align histidine permease (characterized)
to candidate BWI76_RS07360 BWI76_RS07360 phenylalanine transporter
Query= reanno::pseudo3_N2E3:AO353_12275 (468 letters) >FitnessBrowser__Koxy:BWI76_RS07360 Length = 458 Score = 377 bits (968), Expect = e-109 Identities = 193/439 (43%), Positives = 275/439 (62%), Gaps = 6/439 (1%) Query: 8 LKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEMA 67 L RGL RHI+ +ALG AIGTGLF G AIQMAGPAVLL Y + G F++MR LGEM Sbjct: 18 LHRGLQNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYAVAGIVAFLIMRQLGEMV 77 Query: 68 VHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSRWIW 127 V PV+GSF +A Y GP AGF+ GW Y V+VGMA++TA GIYM +W P+V WIW Sbjct: 78 VEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYWLPDVPTWIW 137 Query: 128 VLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGI-MLFGISTAPGQVTDI 186 I+ +NL NV+++GE EFW +L+KV AI+ MI GFG+ MLFG G I Sbjct: 138 AAAFFLIINAVNLVNVRLYGEAEFWFALIKVLAIIGMI--GFGLWMLFG--GHGGSKAGI 193 Query: 187 SNLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRIL 246 NLW GGF G GLI S AV+MF+FGG+E+IG+TA EA++P+ +P+A+N V RIL Sbjct: 194 DNLWKHGGFFATGWHGLIMSLAVIMFSFGGLELIGITAAEAQNPEKSIPKAVNQVVYRIL 253 Query: 247 LFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDIFG 306 LFY+ +++VL++++PW +I S SPFV IF L + A+ LN V++ A++S NS ++ Sbjct: 254 LFYIGSLVVLLALYPWVEIQSDSSPFVMIFHNLDSNVVASALNFVILVASLSVYNSGVYS 313 Query: 307 AGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVFLLIASIA 366 RM+FGL+ QG+APK A +S+ GVP ++++ + L V+LNYL+P+ L+ ++ Sbjct: 314 NSRMLFGLSVQGNAPKFLARVSKRGVPVNSLLLSGIITSLVVVLNYLLPQKALGLLMALV 373 Query: 367 TFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFGVLGYFPD 426 + W+MI + R + + + KF P + IAF+ + ++ Sbjct: 374 VATLLLNWIMICLAHLKFRAAQ-RRKGREPKFKALLSPASNYICIAFLALILVLMCTIDG 432 Query: 427 TQAALIVGVVWIVLLVLAY 445 + + I+ VWI+ L A+ Sbjct: 433 MRLSAILLPVWILFLFAAF 451 Lambda K H 0.329 0.142 0.441 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: 661 Number of extensions: 33 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: 468 Length of database: 458 Length adjustment: 33 Effective length of query: 435 Effective length of database: 425 Effective search space: 184875 Effective search space used: 184875 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 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