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 Ac3H11_3568 TRAP dicarboxylate transporter, DctM subunit, unknown substrate 6
Query= TCDB::D5ATK1 (611 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3568 Length = 594 Score = 646 bits (1667), Expect = 0.0 Identities = 346/576 (60%), Positives = 429/576 (74%), Gaps = 29/576 (5%) Query: 3 MELIAQNMAPIMFVSLIVFLLLGYPVAFSLAANGLVFFIIGVELAPLSGGSINLDWPLLN 62 ME + N+APIMF LI FLL+G+PVAFSL A GL F IG+EL L LL Sbjct: 1 MEFLTHNLAPIMFAGLICFLLVGFPVAFSLGACGLFFAFIGIELNVLPEA-------LLQ 53 Query: 63 AMPERFWGVLSNETLLAIPFFTFMGILLEKSGMAEDLLDTIGQLFGPIRGGLAYAVILVG 122 A+P R +G++ N+TLLAIPFFT MG++LE+SGMAEDLLDTIGQLFGPIRGGLA AVI VG Sbjct: 54 AVPLRIFGIMQNDTLLAIPFFTLMGLILERSGMAEDLLDTIGQLFGPIRGGLALAVIFVG 113 Query: 123 ALLAATTGVVAASVIAMGLISLPIMLRYGYDRRIASGVIAASGTLAQIIPPSLVLIVLAD 182 ALLAATTGVVAASVI+MGLISLPIMLRYGYDRR+A+GVIAASGTLAQIIPPSLVLI++AD Sbjct: 114 ALLAATTGVVAASVISMGLISLPIMLRYGYDRRLAAGVIAASGTLAQIIPPSLVLIIIAD 173 Query: 183 QLGRSVGDMYKGALIPGLVLTGLYMLYVLVMSILRPNSMPALPKEARTLG-----QGVLS 237 Q+GRSVGDMYKGA +PGL+LTG Y LY++++++ +P +PA+P EARTL GV S Sbjct: 174 QMGRSVGDMYKGAFLPGLMLTGFYALYIILLAVFKPQWVPAIPPEARTLRGDDGKSGVPS 233 Query: 238 FFVAMGIGIA--IFVA----AQH-WLAGTGAAKNAG----ILAASIAVIFVYVMALIDKA 286 V GI +A I+VA A H W +G K A +++ V +V A I+K Sbjct: 234 LLVLTGICVAASIYVAKNMPALHSWWSGETVDKVALDETIVVSMCFGVALAFVAASINKI 293 Query: 287 TGLDRMSHLAQQVIIVLIPPLALIFLVLGTIFLGIATPTEGGAMGAVGALILSAVKKRLS 346 T + +S +A++V VLIPPL LIFLVLGTIFLG+ATPTEGGAMGA+GA I++ ++ RL+ Sbjct: 294 TRMGLLSRVAERVTFVLIPPLLLIFLVLGTIFLGVATPTEGGAMGALGAGIMAIIRGRLT 353 Query: 347 LEVVREALAATTRLSAFVMFILLGARVFSLTFYGVNGHIWVEHLLVSLPGGETGFLIFVS 406 L ++++A+ TT+LS FV+FIL+GA +F LTF GV+G +WVEHLL LPGG+ GFLI V+ Sbjct: 354 LSLLKQAITTTTKLSCFVVFILVGATIFGLTFQGVDGPLWVEHLLTGLPGGQLGFLIVVN 413 Query: 407 LLVFFLAFFLDFFELAFIIVPLLVAPAEALGIDLIWFGVILGVNMQTSFMHPPFGFALFF 466 ++VFFLAFFLDFFEL+FI+VPLL A LGIDLIWFGV+L VNMQTSFMHPPFGFALF+ Sbjct: 414 IMVFFLAFFLDFFELSFIVVPLLAPVAHKLGIDLIWFGVLLAVNMQTSFMHPPFGFALFY 473 Query: 467 LRSVAPKVPFLDKVTGKLTEPVKTSQIYWGAVPFVCIQIVMIAVVIAFPQLVMHYKGKPV 526 LRSVAP ++DKVT K+ PV T QIYWGA+PF+CIQ++M+ ++IAFP +V K V Sbjct: 474 LRSVAPAKEYMDKVTKKMIAPVTTPQIYWGAIPFLCIQLLMVGLIIAFPGIVSSGLDKEV 533 Query: 527 --DVSHVTV----TVPGGIGGGLGGGLGMPGGLGLP 556 D+ V + T+PG GM G P Sbjct: 534 AYDLDKVRMEMEATMPGEAAEAADPTAGMEGAAAAP 569 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: 1002 Number of extensions: 55 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: 594 Length adjustment: 37 Effective length of query: 574 Effective length of database: 557 Effective search space: 319718 Effective search space used: 319718 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