Align Amino acid transporter (characterized, see rationale)
to candidate BPHYT_RS33230 BPHYT_RS33230 amino acid permease
Query= uniprot:A0A0H3C3Q5 (483 letters) >FitnessBrowser__BFirm:BPHYT_RS33230 Length = 486 Score = 340 bits (872), Expect = 6e-98 Identities = 185/488 (37%), Positives = 282/488 (57%), Gaps = 21/488 (4%) Query: 9 SFWTRRKAIDTITAGHADS-HQLKKTLSWPHLVALGVGAIVGTGIYTLTGVGAG-LAGPG 66 S+ R+ D + + AD H L K+L + A+G+GAI+G GI+ LTG A AGP Sbjct: 5 SYMARKSVADIVGSADADEGHSLSKSLGAISITAMGIGAIIGAGIFVLTGTAAAQFAGPS 64 Query: 67 VILSFLIAGAVCACAALCYAELSTMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVC 126 ++LSF++ G CA LCY+EL+ M+P GS+YTY+YA +GE AW +GW LILEY + Sbjct: 65 IVLSFVLGGIACAFVGLCYSELAAMLPVCGSSYTYTYATLGEIFAWIIGWDLILEYAMGA 124 Query: 127 AAVAVGWSAHAHGLFKMIGF--PDALLAGPHQ----------GGLINMPAVFISMAVAGL 174 A VAVGWS + L +G P L P G++N+PA+ I + + Sbjct: 125 ATVAVGWSGYIVSLLHNVGISIPPVLATAPGTVIKLADGTTATGIVNLPAIVIIAILTTM 184 Query: 175 LALGTRESATVNMVLVFVKIIALIVFVVLCLPAFNLAHFTPFMPNGFQAHVPEGAAADAA 234 L LGT+ESA +N ++V VK++ ++ F+ L + A++ PF+P G + Sbjct: 185 LVLGTKESARLNNIMVAVKLVVVVAFIALGVFFIKPANWHPFIPAN------TGEFGNFG 238 Query: 235 KVGVMAAASLIFFAFYGFDAVSTAAEETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGA 294 G++ ++++FFAF GFDAVSTAA+E K P+RD+ IGI+GS+ +CT +Y++VA V G Sbjct: 239 MSGILRGSAVVFFAFIGFDAVSTAAQEAKKPQRDMPIGILGSLIICTILYILVAGVLTGL 298 Query: 295 SRTEVFSKSEAPLVFILESLNHGKIAQLVALAAVIALPTVILAFMYGQSRIFFVMARDGL 354 + + P+ ++++ + L+ + A+ L TVIL +YGQSRIFF M+ DGL Sbjct: 299 VPYAELNVPD-PIAKGVDAIGLNWFSILIKIGALTGLTTVILVLLYGQSRIFFTMSTDGL 357 Query: 355 LPRALSKVNAKTGTPVMMTLLTGVLAAVISGLLSLKDIAELANAGTLWAFIAVGASVILL 414 LP ++V+ + TP + +L G + A+++ L + + E+ + GTL+AFI V +VI L Sbjct: 358 LPPLFARVHPRLQTPYLSQILIGSVVAIVAALTPISVLGEMVSIGTLFAFILVCGAVIYL 417 Query: 415 RLREPNRPRVFSTPLWPIVAPAGILGCLYLFLSLPGKTQLYFLYAHLIGAVVYLAYGMRK 474 R + + R F P P+V GIL CL L LP T + + +IG +Y++YG Sbjct: 418 RRSDSDASRPFRVPGVPVVPVLGILFCLLLMAGLPLVTWVRLVVWLVIGMTIYMSYGRNH 477 Query: 475 SVLAQQER 482 S L ER Sbjct: 478 SRLRYPER 485 Lambda K H 0.326 0.138 0.415 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: 682 Number of extensions: 35 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: 483 Length of database: 486 Length adjustment: 34 Effective length of query: 449 Effective length of database: 452 Effective search space: 202948 Effective search space used: 202948 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: 52 (24.6 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