Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized, see rationale)
to candidate GFF3978 HP15_3918 trap-type mannitol/chloroaromatic compound transport system, large permease component
Query= uniprot:Q9KQS1 (453 letters) >FitnessBrowser__Marino:GFF3978 Length = 436 Score = 253 bits (645), Expect = 1e-71 Identities = 163/456 (35%), Positives = 246/456 (53%), Gaps = 37/456 (8%) Query: 2 AVALLFI-LVIGMMIVGVPIAISLGLSSILFLL--WHSDASLASVAQTLFNAFAGHYTLL 58 A+ LLF ++ +++G+P+A LG S++FL W D S VA ++ G +TL+ Sbjct: 5 ALTLLFFGSLLFFLLLGLPLAFVLGGVSVVFLYFTWGFD-SFYMVASQIWGTM-GSFTLV 62 Query: 59 AIPFFILASTFMSTGGVAKRIIRFAIAMVGWFRGGLAIASVVACMMFAALSGSSPATVVA 118 AIP F+ + + GVA+ + R G RGGLA+ ++ C +FAA+ G S A VVA Sbjct: 63 AIPLFVFMAMILERTGVARDLYRMMHLWCGGLRGGLALGTLGICAVFAAMVGISGAAVVA 122 Query: 119 IGSIVIAGMVKNGYSKEFAAGVICNAGTLGILIPPSIVMVVYSAATNVSVGRMFLGGVVP 178 +G+I + M++ GY K A GVI G GILIPPSI+M++Y+ T VSVG+MF G++P Sbjct: 123 MGTIALPSMLERGYDKSMALGVINTGGGWGILIPPSILMILYALITGVSVGKMFAAGIMP 182 Query: 179 GLLAGLMLIIAIYITAR-------IKNLPKQPFVGWKEALKAAKEASWGLLLVVIILGGI 231 G+L LM++ AIYI R LPK+ W E +A + + +VV++LG I Sbjct: 183 GVL--LMVLTAIYIIVRCHLQPELAPALPKEDRGTWPEKFRALRAVLLPIGVVVMVLGSI 240 Query: 232 YGGIFTPTEAAAVAAVYSFFIANFIYRDMGPFADKTNTKPVLVKVVETFVHKDTKATLYD 291 GGI TPTEAAA+ V I+ +YR F K Sbjct: 241 IGGITTPTEAAAM-GVLGALISAAVYRQ--------------------FKWSILKEAAIR 279 Query: 292 AGKLTIMLMFIIANALILKHVLTEERIPQMITESMLSAGLGPITFLIVVNLILLVGGQFM 351 KLT M+M+I+ A ++I M GP +I + +I+ + + Sbjct: 280 TFKLTGMIMWILFAAHAFSAAYQSMGAQELIEGLMNMVPGGPWGIIIAMMVIVFLLAMVL 339 Query: 352 EPSGLLVIVAPLVFPIAIALGIDPIHLGIMMVVNMEIGMITPPVGLNLFVTSGVA--KMS 409 +P G+++I P+ PI +LG DPI GI+ V+NMEIG +TPP G NLF G+ ++ Sbjct: 340 DPVGIMLITLPVFMPIVESLGFDPIWFGILFVINMEIGYMTPPFGFNLFYLKGIVPPSIT 399 Query: 410 MMNVVKAALPWVGVMFLFLIIVTYVPWVSTWLPTLL 445 M ++ K+ +P+V V + +I++ P ++TWLP LL Sbjct: 400 MKDIYKSIIPFVIVEIVGIILIMVFPEIATWLPDLL 435 Lambda K H 0.329 0.142 0.421 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: 556 Number of extensions: 28 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: 453 Length of database: 436 Length adjustment: 32 Effective length of query: 421 Effective length of database: 404 Effective search space: 170084 Effective search space used: 170084 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