Align TctA, component of The tricarboxylate transporter, TctABC (characterized)
to candidate 8501268 DvMF_2001 protein of unknown function DUF112 transmembrane (RefSeq)
Query= TCDB::Q9FA44 (504 letters) >FitnessBrowser__Miya:8501268 Length = 514 Score = 306 bits (783), Expect = 1e-87 Identities = 173/484 (35%), Positives = 275/484 (56%), Gaps = 8/484 (1%) Query: 17 PENLVIALIGCFVGTIVGLLPGLGPINGVAILLPLAFALHLPAESALILLATVYIGCEYG 76 P N+++ + G G IVG LPGL GVA+++P FA+ A S LI+L +Y G YG Sbjct: 15 PLNILLMVAGLTGGIIVGALPGLTATMGVALMVPATFAMD--ATSGLIMLGAIYAGAIYG 72 Query: 77 GRISSILLNVPGDAAAIMTALDGYPMAQQGKGGVALSISAVSSFFGSLIAIGGIILFAPL 136 G S+ L+ PG +++ T DG+P+ Q G+ + L S +SS FG ++ ++ A Sbjct: 73 GSNSACLICTPGTPSSVATTFDGWPLCQAGRADIGLITSLLSSVFGGIVGTVFLLFLAAP 132 Query: 137 LAQWSLAFGPAEYFALMVFAIACLGSMMAQNPLKSFLAALIGLGLATVGVDANTGVYRFT 196 LA+++L FG E F L +F ++ + M + N +K L+ +GL ++TVG+D N GV RFT Sbjct: 133 LARFALQFGGPENFWLCIFGLSTIAVMSSGNMVKGLLSGAMGLLVSTVGIDPNVGVPRFT 192 Query: 197 FDSVHLSDGVQFIVVVIGLFSVSEILLMLEHTSSGQTMVRKTGRMLFNLKEG--AQCIGT 254 F L GV+ I +IGLFS S++L ++ R ++ +C Sbjct: 193 FGYYPLVQGVEVIPAMIGLFSFSQVLYLIGSYKPFIAEYRPAPGAFGHVVRALVGRCKVN 252 Query: 255 TLRSSVIGFFVGVLPGAGATIASAITYMTEKKLSGNSDSFGKGDIRGVAAPEAANNASAC 314 +RSS+IG VG+LPGAG IAS I+Y K+ N + +G G I GVAA E+ANNA Sbjct: 253 LMRSSIIGTLVGMLPGAGGEIASIISYNEAKRWDKNPERYGTGVIEGVAASESANNAVIG 312 Query: 315 GSFIPMLTLGVPGSGTTAVMMGALTLYNITPGPAMFTEQPDIVWGLIAALLIANVMLLIM 374 GS IPMLTLG+PGS AV++GAL I PG +FT D+ + I + N++++ + Sbjct: 313 GSLIPMLTLGIPGSAVAAVILGALLAKGIQPGFKVFTATGDLAYTFIMSQFAVNLLMIPI 372 Query: 375 NIPLIGLFTRMLTIPLWFVVPAIAAVSAVGVYAVHSTTFDLVLMVALGVLGYILRKMHFP 434 + L + T++L+I L FV AI +S +G YA+ ++ D+ +++ G LGY ++ Sbjct: 373 GLLLARIMTKLLSIRLTFVAIAIVVLSVIGSYAIRNSMLDVWIVIIFGFLGYFSGRVGLD 432 Query: 435 MSPLILGFVLGEMLEQNLRRALSISNGN----MAILWQSGVAKALLIMAIMVIVVPPVLR 490 + LG +LG M+E+NL + + +S + + + +S +A L+++ ++ + P +L Sbjct: 433 TGAMALGIILGPMIEENLGKCVHLSRASGGSVINVFLESPIAILLIVLTLLSLATPFLLD 492 Query: 491 LLRK 494 RK Sbjct: 493 WKRK 496 Lambda K H 0.326 0.141 0.414 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: 789 Number of extensions: 44 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: 504 Length of database: 514 Length adjustment: 34 Effective length of query: 470 Effective length of database: 480 Effective search space: 225600 Effective search space used: 225600 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 (21.6 bits) S2: 52 (24.6 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