Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate RR42_RS06530 RR42_RS06530 C4-dicarboxylate ABC transporter
Query= SwissProt::Q9HU16 (427 letters) >FitnessBrowser__Cup4G11:RR42_RS06530 Length = 434 Score = 263 bits (672), Expect = 8e-75 Identities = 149/428 (34%), Positives = 244/428 (57%), Gaps = 6/428 (1%) Query: 4 LFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDS----VRSLAIKLFETSEHYTLLAI 59 + LF++ LM +GVPI VSLGL G + I L + D+ + ++ + Y LLAI Sbjct: 6 IILFVVFLGLMMLGVPIGVSLGLGGLVAIGLSNLDTQMFGLLAVPQNFYAGLGKYPLLAI 65 Query: 60 PFFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVG 119 P F+L G+ GVA+RL+ FA A VG G L + A+L M +SGS PA AAVG Sbjct: 66 PMFVLVGSIFDRSGVAQRLVTFAIAIVGRGPGMLPLVAILVAMFLGGISGSGPANAAAVG 125 Query: 120 SIAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATE-TSVGKLFIAGVVPG 178 + IA M R+GYP A+ A +V A ILIPPS+ ++Y+ SV LF AG++PG Sbjct: 126 GVMIAAMSRAGYPGAYSAAVVGAAAATDILIPPSVAFIIYSVLVPGASVPALFAAGMIPG 185 Query: 179 LLLGLILMVVIYIVARVKKLPAMPRVSLRE-WLASARKALWGLLLMVIILGGIYSGAFTP 237 +L G+ L+V +AR + A+ R + S R+A WGL+ +ILGG+ +G FTP Sbjct: 186 ILAGVALIVPAVWLARKHNMGAIEAGLPRPPFWKSLREAAWGLVAPFLILGGMRAGWFTP 245 Query: 238 TEAAAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQI 297 TEAA VA VY FV + +YR + + + + E+ + + +++ ++A A +FA+ L+T + Sbjct: 246 TEAAVVAVVYGLFVGMVIYRSISMRDLFVIFQEAAETSAVILLVVALAGIFAYALSTLGV 305 Query: 298 PQSIASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHL 357 +A+ + GL + L ++ +L+ G F++ +I LI P+ PIA +P+ Sbjct: 306 IDPLANAIAHSGLGEYGVLALIVALLMTVGMFLDGISIFLIFVPLLLPIANAFHWNPVWF 365 Query: 358 GIIMVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVS 417 G+++ + + +G TPP+ +NL V+ + + + T+ + L+ + V +++V P ++ Sbjct: 366 GVVLTLKVALGQFTPPLAVNLMVSCRIARVRMEETVPWVVWMLLAMFVAMLLVLAFPPLA 425 Query: 418 LALPNWLG 425 LP++LG Sbjct: 426 TWLPDYLG 433 Lambda K H 0.330 0.144 0.425 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: 595 Number of extensions: 34 Number of successful extensions: 3 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: 427 Length of database: 434 Length adjustment: 32 Effective length of query: 395 Effective length of database: 402 Effective search space: 158790 Effective search space used: 158790 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 (21.9 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