Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_011382867.1 AMB_RS02190 C4-dicarboxylate ABC transporter
Query= SwissProt::Q9HU16 (427 letters) >NCBI__GCF_000009985.1:WP_011382867.1 Length = 651 Score = 258 bits (659), Expect = 4e-73 Identities = 160/429 (37%), Positives = 239/429 (55%), Gaps = 21/429 (4%) Query: 12 LLMFIGVPIAVSLGLSGALTILLFSPD-SVRSLAIKLFETSEHYTLLAIPFFLLSGAFMT 70 L+MF G+PIA +LG+ + +LLF P SV ++A +E + +LAIP F+L GA + Sbjct: 220 LVMFSGMPIAFALGVVALIFMLLFMPAASVDTIAQNFYEELANVIILAIPLFILKGATIG 279 Query: 71 TGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGSIAIAGMVRSG 130 + L +A + I GGL +A +AC LFAA++GSSPAT +A+GS I M G Sbjct: 280 RSNAGKDLYSALHAWLHRIPGGLGVANTIACGLFAAMAGSSPATCSAIGSAGIPEMRARG 339 Query: 131 YPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLLLGLILMVVIY 190 Y F AGI+ GTLGIL+PPS+ M++YA A E S+G+LF+AG+ PGLL LI + Y Sbjct: 340 YSPGFAAGIIAAGGTLGILLPPSVTMLLYAVAAEVSLGRLFLAGIGPGLL--LITLFAGY 397 Query: 191 IVARVK-KLPAMPRVSLREWLASA-------------RKALWGLLLMVIILG---GIYSG 233 V R + + R + SA R +W + I+ G +Y+G Sbjct: 398 SVLRYRHEYRRAERAAASHGTHSALLADEHYTTRQKIRMVVWVAPFVTILAGVMVVLYAG 457 Query: 234 AFTPTEAAAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLT 293 TP+E A V AV + V +Y R +L + + + ML+ II ++L+A+V++ Sbjct: 458 WATPSETAGVGAVLALLVIGLMYGIWRPRLLMPILTGTLRESTMLLMIIGMSLLYAYVMS 517 Query: 294 TEQIPQSIASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGID 353 +I Q+ A W+ L LS W L + + ++ G F+ P +IIL+ API P G D Sbjct: 518 HLRISQAAADWIIGLALSKWFLLAAILLFTVVLGFFLPPVSIILMTAPIILPPLKAAGFD 577 Query: 354 PIHLGIIMVVNMEIGLITPPVGLNLFVTSAVT-GMPLGATIRAALPWLMILLVFLIIVTY 412 I G++M V ME+GLI PPVGLN+FV + +PL I LP+++I++V ++ Sbjct: 578 LIWFGVVMTVVMEMGLIHPPVGLNIFVIKNIAPDIPLRDIIWGTLPFVLIMMVAVVACCL 637 Query: 413 IPAVSLALP 421 IP ++ LP Sbjct: 638 IPGIATWLP 646 Score = 25.4 bits (54), Expect = 0.005 Identities = 32/154 (20%), Positives = 66/154 (42%), Gaps = 20/154 (12%) Query: 268 LLESGKLTIMLMFIIANAMLFAHVLTTEQIPQSI---ASWVTELGLSPWMFLLVVNIVLL 324 ++E+G L L+F + ML A + Q QS W+ L+ M LL + ++L Sbjct: 113 VVEAGILAFCLIFAWKSGMLLAEAVHEGQTSQSAWGPPLWIPYSVLTLGMALLALQVMLQ 172 Query: 325 IAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGIIMVVNMEIGLITPPVGLNLFVTSAV 384 + + A+++ F L P+ + + + G+ V L + Sbjct: 173 VGRRSLWLLAVVVAGVAAFL-----LATPPVKPLVSGLPHWLTGIAYATVTLLVM----F 223 Query: 385 TGMPLGATIRAALPWLMILLVFLIIVTYIPAVSL 418 +GMP+ + ++ L+F+++ ++PA S+ Sbjct: 224 SGMPIAFALG------VVALIFMLL--FMPAASV 249 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: 749 Number of extensions: 52 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 427 Length of database: 651 Length adjustment: 35 Effective length of query: 392 Effective length of database: 616 Effective search space: 241472 Effective search space used: 241472 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: 52 (24.6 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