Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate RR42_RS34990 RR42_RS34990 ABC transporter permease
Query= reanno::PV4:5208943 (465 letters) >FitnessBrowser__Cup4G11:RR42_RS34990 Length = 467 Score = 246 bits (628), Expect = 1e-69 Identities = 155/466 (33%), Positives = 254/466 (54%), Gaps = 17/466 (3%) Query: 6 LFISLFLCMLLGMPIAIALGFSSMLTILLFSDDSLASVALKLYESTSEHYTLLAIPFFIL 65 L +S L ML+G+P+AIA+ +S+L I +A ++ E + LLA+PFFIL Sbjct: 4 LIVSFLLLMLVGLPVAIAMAVASLLYIWASGTVPDVILAQRMIAGV-ESFPLLAVPFFIL 62 Query: 66 SSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGSIVIV 125 + ++ G+ RI +FA+ VG +RGGL +++ ++F+ +SG++ A A +G+I I Sbjct: 63 AGNLMNVAGITGRIYNFAVALVGWMRGGLGHVNIIGSVIFSGMSGTAIADAAGLGTIEIK 122 Query: 126 GMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGLMMGLL 185 M GY +FA GV S TLG +IPPS+ ++Y VS +F+AG++PGL++ L Sbjct: 123 AMQDHGYETEFAVGVTAASATLGPIIPPSLPFVIYGMMANVSIGSLFLAGIVPGLVLTLF 182 Query: 186 LMLAIYIVARIKKLPSRPFPGFRPLAISSAKAMGGLAL-IVIVLGSIYGGIASPTEAAAV 244 +M + A + S ++ L +S + LA + I L + +G S AA + Sbjct: 183 MMGTVAWFAHRRGWGSDTAFSWKLLGNASIEIAVVLAFPLAIWLMTRFG--VSTNVAALI 240 Query: 245 ACV-------YAYFIAVFGYRD----IGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKT 293 A V Y F AV IG + + W E + A++ L F+ L +++ Sbjct: 241 ALVVLLALDWYFDFSAVMALMAPVILIGGM-TLGWFTPTEAAVAAVIWAL-FLGLVRYRS 298 Query: 294 PADKEIRHVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLII 353 + + D + + +LFI+ A +FA +LTT + ++++ I+G W FL++ Sbjct: 299 MTLRSLAKATLDTIETTASVLFIVTAASIFAWLLTTSQAAQMLSDAILGFTHNKWVFLLL 358 Query: 354 VNLLLLAAGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNL 413 N+L+L G F++ +A + I+ PIL PI +LGIDPIH G++M +N+ IG+L PP+G+ L Sbjct: 359 ANVLILIVGCFIDTTAAITILVPILLPIVLKLGIDPIHFGLVMTLNLMIGLLHPPLGMVL 418 Query: 414 FVTAGITGRSMGWVIHSCIPWLALLLFFLALITYIPQISLFLPEYI 459 FV A + S+ + +PWL L L ITY P I+L+LP + Sbjct: 419 FVLARVAKLSVERTTVAILPWLVPLFLTLIAITYFPAITLWLPNLV 464 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: 602 Number of extensions: 38 Number of successful extensions: 6 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: 467 Length adjustment: 33 Effective length of query: 432 Effective length of database: 434 Effective search space: 187488 Effective search space used: 187488 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