Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate Echvi_3627 Echvi_3627 TRAP transporter, DctM subunit
Query= reanno::PV4:5208943 (465 letters) >FitnessBrowser__Cola:Echvi_3627 Length = 431 Score = 277 bits (708), Expect = 6e-79 Identities = 165/459 (35%), Positives = 265/459 (57%), Gaps = 39/459 (8%) Query: 1 MTIATLFISLFLCMLLGMPIAIALGFSSMLTILLF--SDDSLASVALKLYESTSEHYTLL 58 +TI L +S M LG+P+A +LGFSS+LT+++ + S+ ++A ++ + ++LL Sbjct: 4 ITIIILVLSFITLMGLGVPVAWSLGFSSLLTLMVTVAAVPSMTTIAQRMGAGLNS-FSLL 62 Query: 59 AIPFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAA 118 AIPFFIL+ ++ GG+A R+I+ A G + GGL +V+A MLF A++GS+ A +A Sbjct: 63 AIPFFILAGEIMNKGGIANRLINLAKALTGKLPGGLLYVNVIAAMLFGAIAGSAVAAASA 122 Query: 119 IGSIVIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATE-VSAARMFMAGLI 177 +G I+ M GYP++ V TS T G++IPPS V++VY+ A+ VS A +F+AG I Sbjct: 123 LGGILGKRMEDEGYPKELGVAVNVTSSTTGLVIPPSNVLIVYSLASGGVSIAALFVAGYI 182 Query: 178 PGLMMGLLLMLAIYIVARIKKLPSRPFPGFRPLAISSAKAMGGLALIVIVLGSIYGGIAS 237 PGL MGLLLML + KKLP+ F+ L A L L+VIV+G I G+ + Sbjct: 183 PGLFMGLLLMLTAAYFIKKKKLPAGEPTSFKELGKVFFSAAPSLTLLVIVIGGIVMGVFT 242 Query: 238 PTEAAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPADK 297 TEA+A+A +Y ++ F Y ++ P + Sbjct: 243 ATEASAIAVLYCLGLSFF-YGELKP----------------------------------R 267 Query: 298 EIRHVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLIIVNLL 357 ++ ++ + + ++ +IA +M + V+++E IP I+ ++ + + LII+NL+ Sbjct: 268 DLPAILLKSSATTAVVAMLIATSMAMSWVMSSEDIPQSISAVLLSLSDNKFVILIIINLI 327 Query: 358 LLAAGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTA 417 LL G FM+ + +LI PI P+ T+LGIDP+H GIIMV+N+ IG+ TPPVG LF+ Sbjct: 328 LLFVGIFMDMTPAVLIFTPIFLPVVTELGIDPVHFGIIMVLNLCIGLCTPPVGSVLFIGV 387 Query: 418 GITGRSMGWVIHSCIPWLALLLFFLALITYIPQISLFLP 456 G+ S+ V+ +P+ ++ LA+IT PQ++L+LP Sbjct: 388 GVAKTSISNVVKPLLPFFIAMIIGLAVITIWPQLTLWLP 426 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: 588 Number of extensions: 33 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: 465 Length of database: 431 Length adjustment: 33 Effective length of query: 432 Effective length of database: 398 Effective search space: 171936 Effective search space used: 171936 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