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_011841207.1 RSPH17029_RS08775 TRAP transporter large permease subunit
Query= TCDB::D5ATK1 (611 letters) >NCBI__GCF_000015985.1:WP_011841207.1 Length = 682 Score = 899 bits (2322), Expect = 0.0 Identities = 474/630 (75%), Positives = 521/630 (82%), Gaps = 26/630 (4%) Query: 2 LMELIAQNMAPIMFVSLIVFLLLGYPVAFSLAANGLVFFIIGVELAPLSGGSINLDWPLL 61 +ME IA NMAPIMF SL++FLLLGYPVAF+LAANGL+FF IGVELAPLS G+I+L W LL Sbjct: 1 MMEFIAVNMAPIMFASLVIFLLLGYPVAFALAANGLLFFFIGVELAPLSEGTISLGWNLL 60 Query: 62 NAMPERFWGVLSNETLLAIPFFTFMGILLEKSGMAEDLLDTIGQLFGPIRGGLAYAVILV 121 MP+RFWGVLSNETLLAIPFFTFMGI+LE+SGMAEDLLDTIGQLFGPIRGGLAYAVI+V Sbjct: 61 GTMPDRFWGVLSNETLLAIPFFTFMGIVLERSGMAEDLLDTIGQLFGPIRGGLAYAVIIV 120 Query: 122 GALLAATTGVVAASVIAMGLISLPIMLRYGYDRRIASGVIAASGTLAQIIPPSLVLIVLA 181 GALLAATTGVVAASVIAMGLISLPIMLRYGYDRRIASGVIAASGTLAQIIPPSLVLIVLA Sbjct: 121 GALLAATTGVVAASVIAMGLISLPIMLRYGYDRRIASGVIAASGTLAQIIPPSLVLIVLA 180 Query: 182 DQLGRSVGDMYKGALIPGLVLTGLYMLYVLVMSILRPNSMPALPKEARTLGQGVLSFFVA 241 DQLGRSVGDMYKGALIPGL+LTG+YM YVLVMSIL+P SMPALP EARTLG GV+S VA Sbjct: 181 DQLGRSVGDMYKGALIPGLILTGIYMGYVLVMSILKPKSMPALPLEARTLGSGVMSLIVA 240 Query: 242 MGIGIAIFVAAQHWLAGTGAAKNAGILAASIAVIFVYVMALIDKATGLDRMSHLAQQVII 301 + + + VA +WLAG AKNA IL A + +Y+ A++D+A G MS LAQQVII Sbjct: 241 LAVAAGVGVATHYWLAGAYGAKNADILGAVAGIAVIYIAAILDRAAGGKLMSRLAQQVII 300 Query: 302 VLIPPLALIFLVLGTIFLGIATPTEGGAMGAVGALILSAVKKRLSLEVVREALAATTRLS 361 VLIPPLALIFLVLGTIFLGIATPTEGGAMGAVGAL+L+ +K RL+L VV +ALA+TTRLS Sbjct: 301 VLIPPLALIFLVLGTIFLGIATPTEGGAMGAVGALLLAGIKGRLNLAVVTQALASTTRLS 360 Query: 362 AFVMFILLGARVFSLTFYGVNGHIWVEHLLVSLPGGETGFLIFVSLLVFFLAFFLDFFEL 421 AFVMFILLGAR+FSLTFYGVNGHIWVEHLL SLPGGE GFLI VS+LVFFLAFFLDFFEL Sbjct: 361 AFVMFILLGARMFSLTFYGVNGHIWVEHLLTSLPGGEYGFLIAVSVLVFFLAFFLDFFEL 420 Query: 422 AFIIVPLLVAPAEALGIDLIWFGVILGVNMQTSFMHPPFGFALFFLRSVAPKVPFLDKVT 481 AFIIVPLL AEALGIDLIWFG+ILGVNMQTSFMHPPFGFALF+LRSVAP+ ++D VT Sbjct: 421 AFIIVPLLAPAAEALGIDLIWFGIILGVNMQTSFMHPPFGFALFYLRSVAPRQSYIDPVT 480 Query: 482 GKLTEPVKTSQIYWGAVPFVCIQIVMIAVVIAFPQLVMHYKGKPVDVSHVTVTVP----- 536 PV T QIYWGAVPFVCIQIVM+A+VI FPQ+VMHYKG PVD S+VT+T+P Sbjct: 481 KARMAPVTTGQIYWGAVPFVCIQIVMVALVILFPQMVMHYKGAPVDTSNVTITLPQMPGL 540 Query: 537 -----GGIGGGLGGGLGMP--------GGLGLPPIGAQPGAVPAPGGLG---GLPP---G 577 GG+GGGLGGGLG P GGLG PP G PG PAP GLG GL P G Sbjct: 541 GGGLGGGLGGGLGGGLGAPGAQPAPGAGGLGAPP-GLAPGQAPAPSGLGAPAGLAPAPGG 599 Query: 578 LGAPAG-QPVTPPAGGASLGIPAPLGLGGA 606 LG P G PV P + A G+ P GL A Sbjct: 600 LGTPPGLAPVAPGSAPAPGGLGVPPGLAPA 629 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: 1354 Number of extensions: 66 Number of successful extensions: 1 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: 682 Length adjustment: 38 Effective length of query: 573 Effective length of database: 644 Effective search space: 369012 Effective search space used: 369012 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: 54 (25.4 bits)
This GapMind analysis is from Apr 10 2024. 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