Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate GFF2081 Psest_2124 TRAP transporter, DctM subunit
Query= reanno::PV4:5208943 (465 letters) >FitnessBrowser__psRCH2:GFF2081 Length = 425 Score = 228 bits (581), Expect = 3e-64 Identities = 141/453 (31%), Positives = 240/453 (52%), Gaps = 39/453 (8%) Query: 1 MTIATLFISLFLCMLLGMPIAIALGF--SSMLTILLFSDDSLASVALKLYESTSEHYTLL 58 MT+ SL M LGMPIA AL S ++ L F D L + L ++ ++ + LL Sbjct: 1 MTVVVFLSSLLGFMTLGMPIAFALLLTGSVLMWYLDFWDVQLLAQNL---QAGADSFPLL 57 Query: 59 AIPFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAA 118 A+PFFIL+ ++ GG++RRII A GH RGGL ++ A +L A++SGS+ A AA Sbjct: 58 AVPFFILAGELMNAGGISRRIIAMAQAYFGHKRGGLGYVAIAASVLLASMSGSALADTAA 117 Query: 119 IGSIVIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIP 178 + ++++ M GYP ++G++ G + +IPPS+ ++Y T S +++F+AG++P Sbjct: 118 LATLLLPMMRERGYPLSSSSGLVAAGGIIAPIIPPSMPFVIYGVVTGTSISQLFLAGMVP 177 Query: 179 GLMMGLLLMLAIYIVARIKKLPSRPFPGFRPLAISSAKAMGGLALIVIVLGSIYGGIASP 238 GL+MG+ L++A ++AR P + L L VI++G + GG+ +P Sbjct: 178 GLIMGMGLIVAWTLIARRIDEPKQEKASAAERRRVLVDGAAALMLPVIIVGGLRGGLFTP 237 Query: 239 TEAAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPADKE 298 TEAA VA VYA ++ YR++ +W E L RA Sbjct: 238 TEAAVVAAVYALAVSTLLYREL------NWAGLVEVLTRA-------------------- 271 Query: 299 IRHVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLIIVNLLL 358 ++ + ++F+ A A + A+++T ++P IA + + ++ + LL+ Sbjct: 272 --------SRTTASVMFLCAAATVSAYMITLAQLPDEIAAMLGPLAQDPKLLMVAIMLLM 323 Query: 359 LAAGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAG 418 +A G ++ + +LI+ P+L PIA + GIDP++ G++ V+ IG++TPPVG L V G Sbjct: 324 IAVGMVLDLTPTILILGPVLAPIAIKAGIDPVYFGVMFVLIGSIGLITPPVGTVLNVVGG 383 Query: 419 ITGRSMGWVIHSCIPWLALLLFFLALITYIPQI 451 I M ++ +P+ + L + L+ +P I Sbjct: 384 IGRLRMETLVRGVMPFFLIYLVIVGLLIAVPSI 416 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: 553 Number of extensions: 36 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: 425 Length adjustment: 32 Effective length of query: 433 Effective length of database: 393 Effective search space: 170169 Effective search space used: 170169 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