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 AZOBR_RS29760 AZOBR_RS29760 C4-dicarboxylate ABC transporter
Query= TCDB::D5ATK1 (611 letters) >FitnessBrowser__azobra:AZOBR_RS29760 Length = 596 Score = 660 bits (1703), Expect = 0.0 Identities = 362/597 (60%), Positives = 443/597 (74%), Gaps = 66/597 (11%) Query: 10 MAPIMFVSLIVFLLLGYPVAFSLAANGLVFFIIGVELAPLSGGSINLDWPLLNAMPERFW 69 MAPIMF +L+ LLLGYPVAF+LAANGL+F +IG+E+ G D L A+PER + Sbjct: 1 MAPIMFATLVGMLLLGYPVAFALAANGLLFGLIGIEI-----GLFRPD--LFQALPERVY 53 Query: 70 GVLSNETLLAIPFFTFMGILLEKSGMAEDLLDTIGQLFGPIRGGLAYAVILVGALLAATT 129 G ++N+ LLA+PFFTFMG++LE+SGMAEDLLDTIGQLFG IRGGLAYAVI VGALLAATT Sbjct: 54 GTMNNDVLLAVPFFTFMGLVLERSGMAEDLLDTIGQLFGSIRGGLAYAVIFVGALLAATT 113 Query: 130 GVVAASVIAMGLISLPIMLRYGYDRRIASGVIAASGTLAQIIPPSLVLIVLADQLGRSVG 189 GVVAASVI+MGLISLPIMLRYGYDRR+ASGVIAASGTLAQIIPPSLVLIV+ADQLGRSVG Sbjct: 114 GVVAASVISMGLISLPIMLRYGYDRRLASGVIAASGTLAQIIPPSLVLIVMADQLGRSVG 173 Query: 190 DMYKGALIPGLVLTGLYMLYVLVMSILRPNSMPALPKEA---------RTLGQ-GVLSFF 239 DMY+ A IPGL+L GLY LYV V+S++ P + P LP EA R + Q G+L+ F Sbjct: 174 DMYEAAFIPGLLLAGLYALYVFVVSMIWPKAAPGLPPEAIAHREPNGARGVWQLGLLALF 233 Query: 240 --------------------VAMGIGIAIFVA--AQHWLAGTGAAK-------NAGILAA 270 V + + +A+ VA A + G GA + A + AA Sbjct: 234 SGAVATWVMGRTDVKSGADYVVLLLSVAVLVAFLAAAFNRGFGAQRLVLQTVATAALTAA 293 Query: 271 -----------------SIAV--IFVYVMALIDKATGLDRMSHLAQQVIIVLIPPLALIF 311 SIA ++ +A++++ATG +S +A+Q V++PPLALIF Sbjct: 294 AAWLTVNEWTTLALIGDSIAAGALYALAVAVVERATGRRLISRMAEQATFVMVPPLALIF 353 Query: 312 LVLGTIFLGIATPTEGGAMGAVGALILSAVKKRLSLEVVREALAATTRLSAFVMFILLGA 371 LVLGTIF+G+ATPTEGGAMGAVGAL L+A+KKRL+ ++VR+A +T +L+AFV+FIL+GA Sbjct: 354 LVLGTIFIGLATPTEGGAMGAVGALALAAMKKRLNFDMVRQATYSTAKLAAFVLFILIGA 413 Query: 372 RVFSLTFYGVNGHIWVEHLLVSLPGGETGFLIFVSLLVFFLAFFLDFFELAFIIVPLLVA 431 RVFSLTFYGVNGHIWVE L+VSLPGG+ GFLI VS++VF LAFFLDFFELAFI++PLL Sbjct: 414 RVFSLTFYGVNGHIWVEELMVSLPGGQMGFLIAVSVMVFLLAFFLDFFELAFIVIPLLAP 473 Query: 432 PAEALGIDLIWFGVILGVNMQTSFMHPPFGFALFFLRSVAPKVPFLDKVTGKLTEPVKTS 491 A+ LGIDL+WFGVIL VNMQTSFMHPPFGF+LFFLRSVAPK+P++D++T K T PV TS Sbjct: 474 AADRLGIDLVWFGVILAVNMQTSFMHPPFGFSLFFLRSVAPKLPYIDRITKKETAPVLTS 533 Query: 492 QIYWGAVPFVCIQIVMIAVVIAFPQLVMHYKGKPVDVSHVTVTVP-GGIGGGLGGGL 547 QIYWGAVPFV IQ+VM+A+VIAFPQ+VMHYK + + G+GG L L Sbjct: 534 QIYWGAVPFVVIQLVMVALVIAFPQMVMHYKSTATKLDDKQIEEQFKGLGGDLNDDL 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: 1017 Number of extensions: 56 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 611 Length of database: 596 Length adjustment: 37 Effective length of query: 574 Effective length of database: 559 Effective search space: 320866 Effective search space used: 320866 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