Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate 206131 DVU0705 TRAP dicarboxylate transporter, putative
Query= SwissProt::Q9HU16 (427 letters) >MicrobesOnline__882:206131 Length = 427 Score = 290 bits (742), Expect = 6e-83 Identities = 164/427 (38%), Positives = 257/427 (60%), Gaps = 4/427 (0%) Query: 1 MTILFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIP 60 MTIL LF L ++MFIGVP+A ++GLS + I + + S+ I ++ Y LLAIP Sbjct: 1 MTIL-LFGLFAVMMFIGVPLATAMGLSATVAIAA-AKLGLLSVPISVYTGVAKYPLLAIP 58 Query: 61 FFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGS 120 F+ +G GVA RL++F A VG +RGGLAIA+++ CM+ +SGS PA AAV Sbjct: 59 MFIFAGMVFERSGVALRLVNFTVALVGPLRGGLAIASIMVCMVLGGISGSGPADAAAVAM 118 Query: 121 IAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAAT-ETSVGKLFIAGVVPGL 179 + I GM +GYP+AF AG++ AG+ ILIPPSI ++Y+ + SV LF AG++PG Sbjct: 119 VMIPGMAAAGYPKAFSAGLIAAAGSTAILIPPSIAFILYSVLVPQASVPALFAAGLIPGF 178 Query: 180 LLGLILMVVIYIVARVKKLPAM-PRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPT 238 L G+ L++ + ++ + S L + ++A+WGLL VIILGGI SG FTPT Sbjct: 179 LAGIALIIPAWALSVRHGFGLVGDDASCGSILIAFKEAIWGLLAPVIILGGIRSGYFTPT 238 Query: 239 EAAAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIP 298 EAA A Y FV FVYR + L ++L+ES +++ ++M IIA + +FA +T Sbjct: 239 EAAVAAVFYGLFVGFFVYRTLTLRGIYELLVESAEVSAVVMMIIALSSVFAWAGSTLGAF 298 Query: 299 QSIASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLG 358 +++ + + + S M LL V +VL+IAG F++ +I+ I PI P+ G + + G Sbjct: 299 EAMGNALIGISTSETMTLLAVVLVLIIAGMFLDGVSILFIFIPILLPVMTHFGWNAVWFG 358 Query: 359 IIMVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSL 418 +IM + + IG TPP+ LNL VT+ + + + T+ L +++ + + +++V ++P ++ Sbjct: 359 VIMTMCLAIGQFTPPLALNLMVTTRIADIGIEETVPWVLWFVLAMTIAMLLVVFVPQLAT 418 Query: 419 ALPNWLG 425 +P LG Sbjct: 419 LVPGHLG 425 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: 511 Number of extensions: 32 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: 427 Length adjustment: 32 Effective length of query: 395 Effective length of database: 395 Effective search space: 156025 Effective search space used: 156025 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