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 YP_004139565.1 Mesci_0342 TRAP dicarboxylate transporter subunit DctM
Query= TCDB::D5ATK1 (611 letters) >NCBI__GCF_000185905.1:YP_004139565.1 Length = 593 Score = 826 bits (2133), Expect = 0.0 Identities = 437/604 (72%), Positives = 491/604 (81%), Gaps = 23/604 (3%) Query: 3 MELIAQNMAPIMFVSLIVFLLLGYPVAFSLAANGLVFFIIGVELAPLSGGSINLDWPLLN 62 ME IAQNMAPIMF SLI+FLL+GYPVAFSLAANGL+FF IGV L+P SGGSINL WPLL+ Sbjct: 1 MEFIAQNMAPIMFASLIIFLLIGYPVAFSLAANGLMFFFIGVLLSPYSGGSINLAWPLLH 60 Query: 63 AMPERFWG--VLSNETLLAIPFFTFMGILLEKSGMAEDLLDTIGQLFGPIRGGLAYAVIL 120 A+P+ F+G V+SN+TLLAIPFFTFMGI+LE+SGMAEDLLDTIGQLFGPIRGGLAYAVI Sbjct: 61 ALPDNFYGSRVMSNDTLLAIPFFTFMGIVLERSGMAEDLLDTIGQLFGPIRGGLAYAVIF 120 Query: 121 VGALLAATTGVVAASVIAMGLISLPIMLRYGYDRRIASGVIAASGTLAQIIPPSLVLIVL 180 VGALLAATTGVVAASVIAMGLISLPIMLRYGYDRR+ASGVIAASGTLAQIIPPSLVLIVL Sbjct: 121 VGALLAATTGVVAASVIAMGLISLPIMLRYGYDRRLASGVIAASGTLAQIIPPSLVLIVL 180 Query: 181 ADQLGRSVGDMYKGALIPGLVLTGLYMLYVLVMSILRPNSMPALPKEARTLGQGVLSFFV 240 ADQLGRSVGDMY GALIPGLVLTGLYM Y+L+MSI+RPNSMPALP EARTLG GV+S V Sbjct: 181 ADQLGRSVGDMYAGALIPGLVLTGLYMSYILIMSIIRPNSMPALPLEARTLGHGVMSLLV 240 Query: 241 AMGIGIAIFVAAQHWLAGTGAAKNAGILAASIAVIFVYVMALIDKATGLDRMSHLAQQVI 300 A+ + A+ AA +LA NA IL A+ V+F+Y++A+ DK + MS LAQQVI Sbjct: 241 ALLVTSAVSYAAYRYLA-PAHGDNADILGATAGVLFIYIVAIADKRLNFNMMSRLAQQVI 299 Query: 301 IVLIPPLALIFLVLGTIFLGIATPTEGGAMGAVGALILSAVKKRLSLEVVREALAATTRL 360 IVLIPPLALIFLVLGTIFLGIATPTEGGAMG+VGAL ++A K RLSL+VV++ALA+TTRL Sbjct: 300 IVLIPPLALIFLVLGTIFLGIATPTEGGAMGSVGALFMAAAKGRLSLDVVKQALASTTRL 359 Query: 361 SAFVMFILLGARVFSLTFYGVNGHIWVEHLLVSLPGGETGFLIFVSLLVFFLAFFLDFFE 420 S+FV+FIL+GARVFSLTFYGVNGHIWVEHLL SLPGGE GFLI V++LVFFLAFFLDFFE Sbjct: 360 SSFVLFILIGARVFSLTFYGVNGHIWVEHLLTSLPGGEVGFLIGVNMLVFFLAFFLDFFE 419 Query: 421 LAFIIVPLLVAPAEALGIDLIWFGVILGVNMQTSFMHPPFGFALFFLRSVAPKVPFLDKV 480 LAFIIVPLL A+ LGIDLIWFGV+LGVNMQTSFMHPPFGFALF+LRSVA +VP+LD++ Sbjct: 420 LAFIIVPLLAPAADKLGIDLIWFGVLLGVNMQTSFMHPPFGFALFYLRSVAARVPYLDRL 479 Query: 481 TGKLTEPVKTSQIYWGAVPFVCIQIVMIAVVIAFPQLVMHYKGKPVDVSHVTVTVPGGIG 540 TGK PV T QIYWGAVPFVCIQ++MI + IAFPQ+VMHYKG VD + VP Sbjct: 480 TGKQIAPVTTGQIYWGAVPFVCIQVIMIGLTIAFPQMVMHYKGTTVDPGTIDYKVP---- 535 Query: 541 GGLGGGLGMPGGLGLPPIGAQP--GAVPAPGGLGGLPPGLGAPAG----QPVTPPAGGAS 594 +P GL P+G P GA PA G P L P P P A Sbjct: 536 -------EVP---GLSPLGTPPADGAAPAGGATAPAAPDLSQPPSFGDPTPAKPAAPQPD 585 Query: 595 LGIP 598 L P Sbjct: 586 LSQP 589 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: 1090 Number of extensions: 49 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: 593 Length adjustment: 37 Effective length of query: 574 Effective length of database: 556 Effective search space: 319144 Effective search space used: 319144 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