Align high affinity cationic amino acid transporter 1 (characterized)
to candidate BPHYT_RS33230 BPHYT_RS33230 amino acid permease
Query= CharProtDB::CH_091324 (622 letters) >FitnessBrowser__BFirm:BPHYT_RS33230 Length = 486 Score = 266 bits (681), Expect = 1e-75 Identities = 149/426 (34%), Positives = 236/426 (55%), Gaps = 28/426 (6%) Query: 13 MLRRKVVDC-----SREESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIV 67 M R+ V D + E LS+ L + A+G+G+ +GAG++VL G A + AGP+IV Sbjct: 7 MARKSVADIVGSADADEGHSLSKSLGAISITAMGIGAIIGAGIFVLTGTAAAQFAGPSIV 66 Query: 68 ISFLIAALASVLAGLCYGEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSS 127 +SF++ +A GLCY E A +P GS+Y Y+Y T+GE++A+I GW+LIL Y +G ++ Sbjct: 67 LSFVLGGIACAFVGLCYSELAAMLPVCGSSYTYTYATLGEIFAWIIGWDLILEYAMGAAT 126 Query: 128 VARAWSATFDELIGKPIGEFSRQHMALNAPGVLAQTPD---------IFAVIIIIILTGL 178 VA WS L+ +G S + APG + + D + A++II ILT + Sbjct: 127 VAVGWSGYIVSLLHN-VG-ISIPPVLATAPGTVIKLADGTTATGIVNLPAIVIIAILTTM 184 Query: 179 LTLGVKESAMVNKIFTCINVLVLCFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEG 238 L LG KESA +N I + ++V+ + G NW + G Sbjct: 185 LVLGTKESARLNNIMVAVKLVVVVAFIALGVFFIKPANWH------------PFIPANTG 232 Query: 239 GFMPFGFSGVLSGAATCFYAFVGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVS 298 F FG SG+L G+A F+AF+GFD ++T +E K PQ+ +P+GI+ SL+IC I Y V+ Sbjct: 233 EFGNFGMSGILRGSAVVFFAFIGFDAVSTAAQEAKKPQRDMPIGILGSLIICTILYILVA 292 Query: 299 AALTLMMPYFCLDIDSPLPGAFKHQGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAM 358 LT ++PY L++ P+ G + IG+L L+T +L ++ R+ + M Sbjct: 293 GVLTGLVPYAELNVPDPIAKGVDAIGLNWFSILIKIGALTGLTTVILVLLYGQSRIFFTM 352 Query: 359 AEDGLLFKFLAKINNRTKTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAA 418 + DGLL A+++ R +TP ++ + G++ A++A L + L +++SIGTL A+ LV Sbjct: 353 STDGLLPPLFARVHPRLQTPYLSQILIGSVVAIVAALTPISVLGEMVSIGTLFAFILVCG 412 Query: 419 CVLVLR 424 V+ LR Sbjct: 413 AVIYLR 418 Score = 74.7 bits (182), Expect = 9e-18 Identities = 46/123 (37%), Positives = 67/123 (54%), Gaps = 9/123 (7%) Query: 479 VEPSKFSGLIVNISAGLLAALIITVCIVAVLGREALAEGTLWAVFVMTGSVLLCMLVTGI 538 V P + + I G + A++ + ++VLG E ++ GTL+A ++ G+V I Sbjct: 365 VHPRLQTPYLSQILIGSVVAIVAALTPISVLG-EMVSIGTLFAFILVCGAV--------I 415 Query: 539 IWRQPESKTKLSFKVPFVPVLPVLSIFVNIYLMMQLDQGTWVRFAVWMLIGFTIYFGYGI 598 R+ +S F+VP VPV+PVL I + LM L TWVR VW++IG TIY YG Sbjct: 416 YLRRSDSDASRPFRVPGVPVVPVLGILFCLLLMAGLPLVTWVRLVVWLVIGMTIYMSYGR 475 Query: 599 WHS 601 HS Sbjct: 476 NHS 478 Lambda K H 0.324 0.138 0.417 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: 743 Number of extensions: 35 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 622 Length of database: 486 Length adjustment: 36 Effective length of query: 586 Effective length of database: 450 Effective search space: 263700 Effective search space used: 263700 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 53 (25.0 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