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 RR42_RS15935 RR42_RS15935 C4-dicarboxylate ABC transporter
Query= TCDB::D5ATK1 (611 letters) >FitnessBrowser__Cup4G11:RR42_RS15935 Length = 582 Score = 418 bits (1074), Expect = e-121 Identities = 265/625 (42%), Positives = 365/625 (58%), Gaps = 103/625 (16%) Query: 10 MAPIMFVSLIVFLLLGYPVAFSLAANGLVFFIIGVELA--PLSGGSINLDWPLLNAMPER 67 M P+MF L+VF+L+G+PVAFSL+A GL F I+ ++ P+S L A+P R Sbjct: 7 MPPLMFGGLVVFMLIGFPVAFSLSAVGLAFGILAIQFGYFPVS---------FLQAVPSR 57 Query: 68 FWG-VLSNETLLAIPFFTFMGILLEKSGMAEDLLDTIGQLFGPIRGGLAYAVILVGALLA 126 +G VL+NE LLAIPFFTFMG +LEK G+AED+LD++GQLFGP+RGGL Y+VI+VG +L Sbjct: 58 VFGSVLANELLLAIPFFTFMGAILEKCGLAEDMLDSMGQLFGPVRGGLGYSVIIVGFILG 117 Query: 127 ATTGVVAASVIAMGLISLPIMLRYGYDRRIASGVIAASGTLAQIIPPSLVLIVLADQL-- 184 A TG VAA VIAM +ISLP+M+RY Y+ + A+GV+AASGT+ Q++PPSLVL+VLADQL Sbjct: 118 AITGTVAAQVIAMAMISLPVMMRYRYNMKYATGVLAASGTITQLVPPSLVLVVLADQLKT 177 Query: 185 ---GRSVGDMYKGALIPGLVLTGLYMLYVLVMSILRPNSMPALPKEARTLGQGVLSFFVA 241 VG MY GA P ++ L+ LY V++ ++P+ +P +P E RTL L Sbjct: 178 PMGSADVGSMYLGAWGPSVIQIALFALYTFVLTRIKPDWLPPVPVEERTLRGWPLWRKCL 237 Query: 242 MGI---GIAIFVAAQHWLAGTGAAKNAGILAASIAVIFVYVMALIDKATG-LDRMSH--- 294 GI + IF+ + G +G + A A++ + L D G LDR + Sbjct: 238 RGIIPCAVLIFLVLGTIMLGIATPTESGAMGAVGALV---LAVLRDPGFGKLDRNIYRIG 294 Query: 295 LAQQVIIVLIP-----------PLALIFLVLGTIFLGIATPTEGGAMGAVGALILSAVKK 343 LA + ++ PLAL++LV+ + L G + A+ LI+ Sbjct: 295 LAATGVAIIAGTVAFGSHAFRIPLALVYLVITWLLL------RAGQLTALRGLII----- 343 Query: 344 RLSLEVVREALAATTRLSAFVMFILLGARVFSLTFYGVNGHIWVEHLLVSLPGGETGFLI 403 EA +T R++A V+FIL+G+ FS+ F GV+G WVEH+ SLPGG GFL+ Sbjct: 344 --------EAYQSTARITAMVVFILIGSTCFSVVFQGVDGGAWVEHMFTSLPGGWIGFLL 395 Query: 404 FVSLLVFFLAFFLDFFELAFIIVPLLVA-----------------PAEALGIDLIWFGVI 446 V+L +FFLAFFLDFFE+AFI+VP+L P A L+WFGV+ Sbjct: 396 VVNLFIFFLAFFLDFFEIAFIVVPMLAPVAVKVLAPVVADSMGGNPEAAATAALVWFGVM 455 Query: 447 LGVNMQTSFMHPPFGFALFFLRSVAPKVPFLDKVTGKLTEPVKTSQIYWGAVPFVCIQIV 506 L VNMQTSFMHPPFGFALF+LR +APK VK+S IYWGA+P+V +Q++ Sbjct: 456 LCVNMQTSFMHPPFGFALFYLRGIAPK-------------EVKSSDIYWGALPWVGLQMI 502 Query: 507 MIAVVIAFPQLVMHY--KGKPVDVSHVTVTVPGGIGGGLGGGLGMPGGLGLPPIGAQPGA 564 M+ +V+ +P LV + KG + VT+P G G GG +P +P ++PG Sbjct: 503 MVVLVMFWPGLVTMFLDKGSLHHSNAAEVTIPLG-GESPGGAASVPA--PVPGGRSEPGT 559 Query: 565 VPAPGGLGGLPPGLGAPA-GQPVTP 588 + P APA +P TP Sbjct: 560 LELP----------AAPADSEPATP 574 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: 955 Number of extensions: 68 Number of successful extensions: 7 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: 582 Length adjustment: 37 Effective length of query: 574 Effective length of database: 545 Effective search space: 312830 Effective search space used: 312830 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