Align neutral amino acid transporter A (characterized)
to candidate RR42_RS33745 RR42_RS33745 C4-dicarboxylate transporter
Query= CharProtDB::CH_091534 (532 letters) >FitnessBrowser__Cup4G11:RR42_RS33745 Length = 452 Score = 128 bits (321), Expect = 5e-34 Identities = 116/450 (25%), Positives = 198/450 (44%), Gaps = 72/450 (16%) Query: 33 RRCAGFLRRQALVLLTVSGVLAGA---GLGAALRGLSLSRTQVTYLAFPGEMLLRMLRMI 89 RR L Q L+ + +G+L G +G+AL+ L G++ +R+++M+ Sbjct: 3 RRLISSLYVQVLIAVA-AGILLGIFMPHIGSALKPL-------------GDIFIRLIKMV 48 Query: 90 ILPLVVCSLVSGAASLDA-SCLGRLGGIAVAYFGLTTLSASALAVALAFIIKPGSGAQ-- 146 P++ ++V G A +++ LGR+G A+ YF + + A L V + +++PG G Sbjct: 49 FAPIIFATVVLGIAKMESMKDLGRVGWRALLYFEVLSTFALLLGVIVVNVVQPGHGMNVD 108 Query: 147 --TLQSSDLGLEDSGPPPVPKETVDSFLDLARNLFPSNLVVAAFRTYATDYKVVTQNSSS 204 TL + + + + + +D NL P +++ A + Sbjct: 109 PATLDTKSIAAYTA------QVKHEGIMDFLLNLVPMSIMDALAKN-------------- 148 Query: 205 GNVTHEKIPIGTEIEGMNILGLVLFALVLGVALKKLGSEGEDLIRFFNSLNEATMVLVSW 264 +IL +++F++ +GVAL LG G+ + +S A +V Sbjct: 149 -----------------DILQILVFSVFMGVALAHLGERGKPFVAALDSFANAMFAIVGM 191 Query: 265 IMWYVPVG----IMFLVGSKIVEMKDIIVLVTSLGKYIFASILGHVIHGGIVLPLIYFVF 320 IM PV + F VG K + SLGK + + IVL I + Sbjct: 192 IMRVAPVAAFGAMSFTVG------KYGFGSIASLGKLVATMYGTCALFVLIVLGAICRI- 244 Query: 321 TRKNPFRFLLGLLAPFATAFATCSSSATLPSMMKCIEENNGVDKRISRFILPIGATVNMD 380 F FL + T T SS + +P +M+ +E N GV K + ++P G T N D Sbjct: 245 CGFGLFNFLKYIKDEILTVLGTSSSESVIPQLMRKLE-NVGVSKPVVGLVVPAGLTFNPD 303 Query: 381 GAAIFQCVAAVFIAQLNNVELNAGQIFTILVTATASSVGAAGVPAGGVLTIAIILEAIG- 439 G I+ +AA+FIAQ N L F +L +S G+AG+ G +T+A L ++G Sbjct: 304 GQCIYYTMAAIFIAQATNTPLTLTDQFVVLGVLLLTSKGSAGITGSGFITLAATLASLGK 363 Query: 440 LPTHDLPLILAVDWIVDRTTTVVNVEGDAL 469 +P + L+L VD + + N G+A+ Sbjct: 364 IPVAGMVLLLGVDRFMSEARAITNTIGNAV 393 Lambda K H 0.320 0.136 0.390 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: 384 Number of extensions: 15 Number of successful extensions: 2 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: 532 Length of database: 452 Length adjustment: 34 Effective length of query: 498 Effective length of database: 418 Effective search space: 208164 Effective search space used: 208164 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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