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 SMc04249 SMc04249 hypothetical protein
Query= TCDB::D5ATK1 (611 letters) >FitnessBrowser__Smeli:SMc04249 Length = 597 Score = 841 bits (2172), Expect = 0.0 Identities = 441/597 (73%), Positives = 504/597 (84%), Gaps = 25/597 (4%) Query: 2 LMELIAQNMAPIMFVSLIVFLLLGYPVAFSLAANGLVFFIIGVELAPLSGGSINLDWPLL 61 ++E +A+N+APIMFVSLIVFLLLGYPVAFSLAANGL+FFIIGVELAPLS SINL WPLL Sbjct: 1 MIEFVAENLAPIMFVSLIVFLLLGYPVAFSLAANGLLFFIIGVELAPLSD-SINLSWPLL 59 Query: 62 NAMPERFWGVLSNETLLAIPFFTFMGILLEKSGMAEDLLDTIGQLFGPIRGGLAYAVILV 121 NA+PERFWGV+SN+TLLAIPFFTFMGI+LE+SGMAEDLLDTIGQLFGP+RGGLAYAVI V Sbjct: 60 NALPERFWGVMSNDTLLAIPFFTFMGIVLERSGMAEDLLDTIGQLFGPVRGGLAYAVIFV 119 Query: 122 GALLAATTGVVAASVIAMGLISLPIMLRYGYDRRIASGVIAASGTLAQIIPPSLVLIVLA 181 GALLAATTGVVAASVIAMGLISLPIMLRYGYDRRIASGVIAASGTLAQIIPPSLVLIVLA Sbjct: 120 GALLAATTGVVAASVIAMGLISLPIMLRYGYDRRIASGVIAASGTLAQIIPPSLVLIVLA 179 Query: 182 DQLGRSVGDMYKGALIPGLVLTGLYMLYVLVMSILRPNSMPALPKEARTLGQGVLSFFVA 241 DQLGRSVGDMY GALIPGLVLTGLYM Y+L+M+ ++ +SMPALP EARTLG GV S +A Sbjct: 180 DQLGRSVGDMYAGALIPGLVLTGLYMGYILLMTFVKRHSMPALPLEARTLGSGVASLAIA 239 Query: 242 MGIGIAIFVAAQHWLAGTGAAKNAGILAASIAVIFVYVMALIDKATGLDRMSHLAQQVII 301 + + AI AA +L+ T +NA IL A++ +IF+Y+ AL D+ ++ +S LAQQVII Sbjct: 240 LLVACAIAYAAHVYLSPT-QGENADILGATVGIIFIYLAALADRTLKINALSRLAQQVII 298 Query: 302 VLIPPLALIFLVLGTIFLGIATPTEGGAMGAVGALILSAVKKRLSLEVVREALAATTRLS 361 VLIPPLALIFLVLGTIFLGIATPTEGGAMGAVGAL+++A K RL++EVVR ALA+TTRLS Sbjct: 299 VLIPPLALIFLVLGTIFLGIATPTEGGAMGAVGALVMAAGKGRLNMEVVRAALASTTRLS 358 Query: 362 AFVMFILLGARVFSLTFYGVNGHIWVEHLLVSLPGGETGFLIFVSLLVFFLAFFLDFFEL 421 AFV+FIL+GARVFSLTFYGVNGH+WVEHLL +LPGGE GFLI V++LVFFLAFFLDFFEL Sbjct: 359 AFVLFILIGARVFSLTFYGVNGHLWVEHLLTALPGGEIGFLIAVNVLVFFLAFFLDFFEL 418 Query: 422 AFIIVPLLVAPAEALGIDLIWFGVILGVNMQTSFMHPPFGFALFFLRSVAPKVPFLDKVT 481 AFIIVPLL A+ LGIDLIWFGV+LG+NMQTSFMHPPFGFALF+LRSVA +VP+LD+VT Sbjct: 419 AFIIVPLLAPAADKLGIDLIWFGVLLGINMQTSFMHPPFGFALFYLRSVAARVPYLDRVT 478 Query: 482 GKLTEPVKTSQIYWGAVPFVCIQIVMIAVVIAFPQLVMHYKGK--PVDVSHVTVTVPG-G 538 GK+ +PV T QIYWGAVPFVCIQ+VM+A+ + FPQ+V+HYKG VD S + + VPG G Sbjct: 479 GKMMQPVTTGQIYWGAVPFVCIQVVMVALTLMFPQMVLHYKGSGAAVDPSTIKIEVPGFG 538 Query: 539 IGGG------LGGGLGMPGGLGLPPIGAQPGAVPAPGGLGGLPPGLGAPAGQPVTPP 589 GGG GGGLG+PGGL L PG P GG G QP T P Sbjct: 539 TGGGGLTLPDNGGGLGLPGGLQL------PGGSPLDGG--------GQQPAQPNTAP 581 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: 1113 Number of extensions: 45 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: 597 Length adjustment: 37 Effective length of query: 574 Effective length of database: 560 Effective search space: 321440 Effective search space used: 321440 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 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