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_004313532.1 C665_RS13030 TRAP transporter permease DctM
Query= TCDB::D5ATK1 (611 letters) >NCBI__GCF_000310185.1:WP_004313532.1 Length = 547 Score = 639 bits (1647), Expect = 0.0 Identities = 325/525 (61%), Positives = 416/525 (79%), Gaps = 26/525 (4%) Query: 2 LMELIAQNMAPIMFVSLIVFLLLGYPVAFSLAANGLVFFIIGVELAPLSGGSINLDWPLL 61 + E + NMAP+MF S+++FLL G+PVAF+LAANG++F ++G+EL L G L Sbjct: 1 MTEFLVANMAPLMFASMVLFLLFGFPVAFALAANGILFGLVGIELGLLHGA-------LF 53 Query: 62 NAMPERFWGVLSNETLLAIPFFTFMGILLEKSGMAEDLLDTIGQLFGPIRGGLAYAVILV 121 A+PER +G+++N+TLLA+PFFTFMG++LE+SGMAEDLLDTIGQLFGPIRGGLA+AVI V Sbjct: 54 QALPERIFGIMANDTLLAVPFFTFMGLVLERSGMAEDLLDTIGQLFGPIRGGLAFAVIFV 113 Query: 122 GALLAATTGVVAASVIAMGLISLPIMLRYGYDRRIASGVIAASGTLAQIIPPSLVLIVLA 181 GALLAATTGVVAASVI+MGLISLPIMLRYGYD R+A+GVIAASGTLAQIIPPSLVLIV+A Sbjct: 114 GALLAATTGVVAASVISMGLISLPIMLRYGYDHRLATGVIAASGTLAQIIPPSLVLIVMA 173 Query: 182 DQLGRSVGDMYKGALIPGLVLTGLYMLYVLVMSILRPNSMPALPKEARTL-----GQGVL 236 DQLGRSVGDMY+GAL+PGLVLTG+Y+ YV +++ILRP+ PA+P EARTL G+ Sbjct: 174 DQLGRSVGDMYQGALLPGLVLTGMYVAYVALVAILRPSHAPAMPLEARTLREPDGASGMR 233 Query: 237 SFFVAMGIGIA-IFVAAQHWLAGTGAAKNAGILAASIAVIFVYVMALIDKATGLDRMSHL 295 S V + +A ++ A +++A + + +V A+I++ G+ +S + Sbjct: 234 SLAVLTLVSVAGAWLFASQLYRADAPRDEVVVVSAMVGIGIAFVAAMINRLFGIGLLSRM 293 Query: 296 AQQVIIVLIPPLALIFLVLGTIFLGIATPTEGGAMGAVGALILSAVKKRLSLEVVREALA 355 A++V VLIPPL LIFLVLGTIF+G+ATPTEGGAMGA+GA++++ ++RLSL ++++A+ Sbjct: 294 AERVTFVLIPPLGLIFLVLGTIFIGVATPTEGGAMGALGAVLMALARRRLSLPLLKQAMD 353 Query: 356 ATTRLSAFVMFILLGARVFSLTFYGVNGHIWVEHLLVSLPGGETGFLIFVSLLVFFLAFF 415 +TT+LS FV+FIL+G+ VF LTF GVNG +WVEHL+ SLPGG+TGFL+ V+LLVF LAFF Sbjct: 354 STTKLSCFVIFILIGSSVFGLTFRGVNGDLWVEHLMTSLPGGQTGFLVAVNLLVFVLAFF 413 Query: 416 LDFFELAFIIVPLLVAPAEALGIDLIWFGVILGVNMQTSFMHPPFGFALFFLRSVAPKVP 475 LD+FELAFIIVPLL A+ LGIDLIWFGV+L VNMQTSF+HPPFGFALFFLRSVA Sbjct: 414 LDYFELAFIIVPLLAPVADKLGIDLIWFGVLLAVNMQTSFLHPPFGFALFFLRSVA---- 469 Query: 476 FLDKVTGKLTEPVKTSQIYWGAVPFVCIQIVMIAVVIAFPQLVMH 520 +E VKT+ IYWGAVPFV IQ+VM+ ++IAFP LV + Sbjct: 470 ---------SEKVKTASIYWGAVPFVIIQLVMVGLIIAFPGLVSY 505 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: 967 Number of extensions: 51 Number of successful extensions: 4 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: 547 Length adjustment: 36 Effective length of query: 575 Effective length of database: 511 Effective search space: 293825 Effective search space used: 293825 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