Align TRAP C4-dicarboxylate transport system permease, DctM-2 subunit, component of The 2-ketomonocarboxylate transporter (presented in order of affinity - 2-oxovalerate [highest affinity, KD=0.1 μM], 2-oxoisovalerate, 2-oxobutyrate, 2-oxoisocaproate, 2-oxo-3-methylvalerate, pyruvate [lowest affinity, KD=3 μM]) (characterized)
to candidate WP_004313523.1 C665_RS13005 TRAP transporter permease DctM
Query= TCDB::D5ATK1 (611 letters) >NCBI__GCF_000310185.1:WP_004313523.1 Length = 603 Score = 601 bits (1549), Expect = e-176 Identities = 323/599 (53%), Positives = 419/599 (69%), Gaps = 27/599 (4%) Query: 2 LMELIAQNMAPIMFVSLIVFLLLGYPVAFSLAANGLVFFIIGVELAPLSGGSINLDWPLL 61 ++EL + +MF SL+ FLL G+PVAF+LAA GL+F IGVE+ LS + Sbjct: 1 MIELFTAHAPELMFGSLLAFLLTGFPVAFALAACGLLFGFIGVEIGLLSPS-------IF 53 Query: 62 NAMPERFWGVLSNETLLAIPFFTFMGILLEKSGMAEDLLDTIGQLFGPIRGGLAYAVILV 121 A+P R +G++ N+TLLAIPFFT MG++LE+SGMAE+LLDT+GQ+FGPIRGGLA AVI V Sbjct: 54 QALPLRVFGIIQNDTLLAIPFFTLMGLVLERSGMAEELLDTVGQVFGPIRGGLALAVIFV 113 Query: 122 GALLAATTGVVAASVIAMGLISLPIMLRYGYDRRIASGVIAASGTLAQIIPPSLVLIVLA 181 GALLAATTGVVAA+VI+MGLISLPIMLRYGY IASG I ASGTLAQI+PPSLVLIV+A Sbjct: 114 GALLAATTGVVAAAVISMGLISLPIMLRYGYSPAIASGAITASGTLAQIVPPSLVLIVIA 173 Query: 182 DQLGRSVGDMYKGALIPGLVLTGLYMLYVLVMSILRPNSMPALPKEARTLGQ-------- 233 DQLGRSVGD+YKGA IP +L GLY+L+++ ++I +P +PALP EAR+ + Sbjct: 174 DQLGRSVGDLYKGAFIPAFILIGLYVLFIIGLAIFKPAMVPALPPEARSYREPDGSSGMR 233 Query: 234 --GVLSFFVA-----MGIGIAIFVAAQHWLAGTGAAKNAGILAASIAVIFVYVMALIDKA 286 GV + FV G+ + ++A A ++A + +F + A+++K Sbjct: 234 SLGVFTLFVTAVSVTFGMYYSEILSAFKGTEVKAALDETIVVALTGGTLFAFAAAMVNKV 293 Query: 287 TGLDRMSHLAQQVIIVLIPPLALIFLVLGTIFLGIATPTEGGAMGAVGALILSAVKKRLS 346 TG+ +S + ++V VLIPPLALIFLVLGTIFLG+ATPTEGGAMGAVG +I++ + +L Sbjct: 294 TGMGLLSRITERVTFVLIPPLALIFLVLGTIFLGVATPTEGGAMGAVGGMIMAFSRGKLD 353 Query: 347 LEVVREALAATTRLSAFVMFILLGARVFSLTFYGVNGHIWVEHLLVSLPGGETGFLIFVS 406 + +++ L +T RLS FVMFIL+G+ +FS TF V+G IWVEHL LPGGE GFL+FV+ Sbjct: 354 MTLLKHGLESTARLSCFVMFILIGSTIFSFTFTAVDGPIWVEHLFDKLPGGEIGFLVFVN 413 Query: 407 LLVFFLAFFLDFFELAFIIVPLLVAPAEALGIDLIWFGVILGVNMQTSFMHPPFGFALFF 466 ++FFL FF+DFFE+AFI+VPLL A+ LGIDL+WFGV+L +N+QTSF+ PPFGFALF+ Sbjct: 414 TVIFFLGFFIDFFEIAFILVPLLAPVADKLGIDLVWFGVLLAMNLQTSFLTPPFGFALFY 473 Query: 467 LRSVAPKVPFLDKVTGKLTEPVKTSQIYWGAVPFVCIQIVMIAVVIAFPQLVMHYKGKPV 526 LRSVAP +LD+VT K VKT IY G++PFV +QIVM+ +IAFP LV K + Sbjct: 474 LRSVAPAKDYLDRVTKKRVAGVKTMDIYAGSIPFVLMQIVMVVALIAFPGLVTFTLDKKM 533 Query: 527 DVSHVTVTVP---GGIGGGLGGGLGMPGGLGLPPIGAQPGAVPAPGGLGGLPPGLGAPA 582 +V T+ + GG GGG G G G P A+P AP G G P G A A Sbjct: 534 EVDLDTIEIKVDGGGDGGGWGAQQSDSWGGGASP--AEPPGSAAPEGSGTPPSGEPAAA 590 Lambda K H 0.327 0.146 0.437 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: 1023 Number of extensions: 47 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: 611 Length of database: 603 Length adjustment: 37 Effective length of query: 574 Effective length of database: 566 Effective search space: 324884 Effective search space used: 324884 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 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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