Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate BPHYT_RS33230 BPHYT_RS33230 amino acid permease
Query= TCDB::S6EX81 (469 letters) >FitnessBrowser__BFirm:BPHYT_RS33230 Length = 486 Score = 288 bits (738), Expect = 2e-82 Identities = 163/470 (34%), Positives = 259/470 (55%), Gaps = 15/470 (3%) Query: 7 ADFELYRDADKHYN--QVLTTRDFLALGVGTIISTSIFTLPGQVAAQFAGPGVVFSYLLA 64 AD DAD+ ++ + L A+G+G II IF L G AAQFAGP +V S++L Sbjct: 13 ADIVGSADADEGHSLSKSLGAISITAMGIGAIIGAGIFVLTGTAAAQFAGPSIVLSFVLG 72 Query: 65 ALVAGFVALAYAEMSTVMPFAGSAYSWISVLFGEGFGWIAGWALLAEYFIAVAFVGSGFS 124 + FV L Y+E++ ++P GS+Y++ GE F WI GW L+ EY + A V G+S Sbjct: 73 GIACAFVGLCYSELAAMLPVCGSSYTYTYATLGEIFAWIIGWDLILEYAMGAATVAVGWS 132 Query: 125 ANLQQLLAPLGFHLPKVLANPFGT-----DG----GVVDIISLLVILLSAIIVFRGASDA 175 + LL +G +P VLA GT DG G+V++ ++++I + ++ G ++ Sbjct: 133 GYIVSLLHNVGISIPPVLATAPGTVIKLADGTTATGIVNLPAIVIIAILTTMLVLGTKES 192 Query: 176 GRISQILVVLKVAAVIAFIIVGITVIKPANYHPFIPPHNPKTGFGGFSGIWSGVSMIFLA 235 R++ I+V +K+ V+AFI +G+ IKPAN+HPFIP + + G G SGI G +++F A Sbjct: 193 ARLNNIMVAVKLVVVVAFIALGVFFIKPANWHPFIPANTGEFGNFGMSGILRGSAVVFFA 252 Query: 236 YIGFDSIAANSAEAKNPQKTMPRGIIGSLLIAVVLFAAVTLVLVGMHPYSAYAGNAAPVG 295 +IGFD+++ + EAK PQ+ MP GI+GSL+I +L+ V VL G+ PY A P+ Sbjct: 253 FIGFDAVSTAAQEAKKPQRDMPIGILGSLIICTILYILVAGVLTGLVPY-AELNVPDPIA 311 Query: 296 WALQQSGYSVLSEVVTAIALAGMFIALLGMVLAGSRLLYAFGRDGLLPKGLGKMNAR-NL 354 + G + S ++ AL G+ +L ++ SR+ + DGLLP +++ R Sbjct: 312 KGVDAIGLNWFSILIKIGALTGLTTVILVLLYGQSRIFFTMSTDGLLPPLFARVHPRLQT 371 Query: 355 PANGVWTLAIVAIVIGAFFPFAFLAQLISAGTLIAFMFVTLGIYSLRRRQGKDLPEATYK 414 P + V ++ A P + L +++S GTL AF+ V + LRR ++ Sbjct: 372 PYLSQILIGSVVAIVAALTPISVLGEMVSIGTLFAFILVCGAVIYLRRSDSD--ASRPFR 429 Query: 415 MPFYPVLPALGFIGSLFVFWGLDVQAKLYSGIWFLIGILIYFAYGNRRSR 464 +P PV+P LG + L + GL + + +W +IG+ IY +YG SR Sbjct: 430 VPGVPVVPVLGILFCLLLMAGLPLVTWVRLVVWLVIGMTIYMSYGRNHSR 479 Lambda K H 0.328 0.143 0.433 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: 621 Number of extensions: 37 Number of successful extensions: 5 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: 469 Length of database: 486 Length adjustment: 34 Effective length of query: 435 Effective length of database: 452 Effective search space: 196620 Effective search space used: 196620 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