Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate RR42_RS06530 RR42_RS06530 C4-dicarboxylate ABC transporter
Query= reanno::PV4:5208943 (465 letters) >FitnessBrowser__Cup4G11:RR42_RS06530 Length = 434 Score = 221 bits (563), Expect = 4e-62 Identities = 144/467 (30%), Positives = 237/467 (50%), Gaps = 55/467 (11%) Query: 6 LFISLFLCMLLGMPIAIALGFSSMLTILLFSDDS----LASVALKLYESTSEHYTLLAIP 61 LF+ M+LG+PI ++LG ++ I L + D+ L +V Y + Y LLAIP Sbjct: 8 LFVVFLGLMMLGVPIGVSLGLGGLVAIGLSNLDTQMFGLLAVPQNFYAGLGK-YPLLAIP 66 Query: 62 FFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGS 121 F+L + GVA+R++ FA+ VG G L + +++ M +SGS PA AA+G Sbjct: 67 MFVLVGSIFDRSGVAQRLVTFAIAIVGRGPGMLPLVAILVAMFLGGISGSGPANAAAVGG 126 Query: 122 IVIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATE-VSAARMFMAGLIPGL 180 ++I M RAGYP ++A V+ + ILIPPS+ ++Y+ S +F AG+IPG+ Sbjct: 127 VMIAAMSRAGYPGAYSAAVVGAAAATDILIPPSVAFIIYSVLVPGASVPALFAAGMIPGI 186 Query: 181 MMGLLLMLAIYIVARIKKL----PSRPFPGFRPLAISSAKAMGGLALIVIVLGSIYGGIA 236 + G+ L++ +AR + P P P S +A GL ++LG + G Sbjct: 187 LAGVALIVPAVWLARKHNMGAIEAGLPRP---PFWKSLREAAWGLVAPFLILGGMRAGWF 243 Query: 237 SPTEAAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPAD 296 +PTEAA VA VY F+ + YR ++S RD + +F Sbjct: 244 TPTEAAVVAVVYGLFVGMVIYR------SISMRD----------------LFVIF----- 276 Query: 297 KEIRHVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLIIVNL 356 ++ A+ S ++L ++A A +FA+ L+T + +A I GL +G L ++ Sbjct: 277 -------QEAAETSAVILLVVALAGIFAYALSTLGVIDPLANAIAHSGLGEYGVLALIVA 329 Query: 357 LLLAAGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVT 416 LL+ G F++ +I LI P+L PIA +P+ G+++ + + +G TPP+ +NL V+ Sbjct: 330 LLMTVGMFLDGISIFLIFVPLLLPIANAFHWNPVWFGVVLTLKVALGQFTPPLAVNLMVS 389 Query: 417 AGITGRSMGWVIHSCIPWLA--LLLFFLA--LITYIPQISLFLPEYI 459 I M +PW+ LL F+A L+ P ++ +LP+Y+ Sbjct: 390 CRIARVRM----EETVPWVVWMLLAMFVAMLLVLAFPPLATWLPDYL 432 Lambda K H 0.330 0.144 0.424 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: 639 Number of extensions: 44 Number of successful extensions: 4 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: 465 Length of database: 434 Length adjustment: 33 Effective length of query: 432 Effective length of database: 401 Effective search space: 173232 Effective search space used: 173232 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