Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate Echvi_3627 Echvi_3627 TRAP transporter, DctM subunit
Query= SwissProt::Q9HU16 (427 letters) >FitnessBrowser__Cola:Echvi_3627 Length = 431 Score = 310 bits (794), Expect = 6e-89 Identities = 167/429 (38%), Positives = 265/429 (61%), Gaps = 4/429 (0%) Query: 1 MTILFLFLLLFLLMFIGVPIAVSLGLSGALTILLF--SPDSVRSLAIKLFETSEHYTLLA 58 +TI+ L L LM +GVP+A SLG S LT+++ + S+ ++A ++ ++LLA Sbjct: 4 ITIIILVLSFITLMGLGVPVAWSLGFSSLLTLMVTVAAVPSMTTIAQRMGAGLNSFSLLA 63 Query: 59 IPFFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAV 118 IPFF+L+G M GG+A RLI+ A A G + GGL V+A MLF A++GS+ A +A+ Sbjct: 64 IPFFILAGEIMNKGGIANRLINLAKALTGKLPGGLLYVNVIAAMLFGAIAGSAVAAASAL 123 Query: 119 GSIAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATE-TSVGKLFIAGVVP 177 G I M GYP+ G + + T G++IPPS V++VY+ A+ S+ LF+AG +P Sbjct: 124 GGILGKRMEDEGYPKELGVAVNVTSSTTGLVIPPSNVLIVYSLASGGVSIAALFVAGYIP 183 Query: 178 GLLLGLILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTP 237 GL +GL+LM+ + KKLPA S +E A L L+VI++GGI G FT Sbjct: 184 GLFMGLLLMLTAAYFIKKKKLPAGEPTSFKELGKVFFSAAPSLTLLVIVIGGIVMGVFTA 243 Query: 238 TEAAAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQI 297 TEA+A+A +Y ++ F Y +++ + P +LL+S T ++ +IA +M + V+++E I Sbjct: 244 TEASAIAVLYCLGLSFF-YGELKPRDLPAILLKSSATTAVVAMLIATSMAMSWVMSSEDI 302 Query: 298 PQSIASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHL 357 PQSI++ + L + ++ L+++N++LL G FM+ + +LI PIF P+ ELGIDP+H Sbjct: 303 PQSISAVLLSLSDNKFVILIIINLILLFVGIFMDMTPAVLIFTPIFLPVVTELGIDPVHF 362 Query: 358 GIIMVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVS 417 GIIMV+N+ IGL TPPVG LF+ V + ++ LP+ + +++ L ++T P ++ Sbjct: 363 GIIMVLNLCIGLCTPPVGSVLFIGVGVAKTSISNVVKPLLPFFIAMIIGLAVITIWPQLT 422 Query: 418 LALPNWLGM 426 L LP+ G+ Sbjct: 423 LWLPSLFGL 431 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: 538 Number of extensions: 39 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: 427 Length of database: 431 Length adjustment: 32 Effective length of query: 395 Effective length of database: 399 Effective search space: 157605 Effective search space used: 157605 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 Apr 09 2024. 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