Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate Ac3H11_3955 TRAP-type C4-dicarboxylate transport system, large permease component
Query= SwissProt::Q9HU16 (427 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3955 Length = 427 Score = 348 bits (893), Expect = e-100 Identities = 188/428 (43%), Positives = 272/428 (63%), Gaps = 3/428 (0%) Query: 1 MTILFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIP 60 M L L F+LM IGVPIA SLGLS AL L+ + ++ I++ ++LLAIP Sbjct: 1 MDTLVLLGTFFVLMMIGVPIAYSLGLS-ALAGALWIDLPLDAVMIQVASGVNKFSLLAIP 59 Query: 61 FFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGS 120 FF+L+GA M GG+ARRL+ FA VG IRGGL++ +LA F A+SGSS A A++GS Sbjct: 60 FFVLAGAIMAEGGMARRLVAFAGVLVGFIRGGLSLVNILASTFFGAISGSSVADTASIGS 119 Query: 121 IAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVY--AAATETSVGKLFIAGVVPG 178 + I M + GYP+ F + + ILIPPS V+Y AA S+ LF+AGV+PG Sbjct: 120 VLIPEMEKKGYPRPFATAVTVSGSVQAILIPPSHNAVLYSLAAGGTVSIAALFMAGVLPG 179 Query: 179 LLLGLILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPT 238 LL+GL L + A + P + L++ L +ALWGL+ MVIILGGI SG FT Sbjct: 180 LLMGLTLAALCLFTAHREGYPKGEVIPLKQALKICVEALWGLMTMVIILGGILSGVFTAN 239 Query: 239 EAAAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIP 298 E+A++A V++ FV +F+YRD + + PK++ + K ++M +I A F +++T IP Sbjct: 240 ESASIAVVWAFFVTMFIYRDYKWRDLPKLVHRTVKTVTVVMILIGFAAAFGYLMTMMMIP 299 Query: 299 QSIASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLG 358 + +++T L + ++ L ++NI+LL+ G M+ S +ILIL PI P+ LG+DP+H G Sbjct: 300 MKVTAFLTSLSDNKYVILAMINIMLLLLGCLMDMSPLILILTPILLPVVKMLGVDPVHFG 359 Query: 359 IIMVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSL 418 +IM+VN+ IGLITPPVG LF +AV +PLG RA +P+ + L V L++VTY+PA+SL Sbjct: 360 MIMMVNLGIGLITPPVGTVLFTGAAVAKLPLGIVTRAMMPFFVALFVVLLMVTYVPAISL 419 Query: 419 ALPNWLGM 426 LP +G+ Sbjct: 420 WLPRAMGL 427 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: 478 Number of extensions: 21 Number of successful extensions: 6 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