Align TctA, component of The tricarboxylate transporter, TctABC (characterized)
to candidate WP_086509277.1 BZY95_RS07220 Tat pathway signal protein
Query= TCDB::Q9FA44 (504 letters) >NCBI__GCF_002151265.1:WP_086509277.1 Length = 504 Score = 313 bits (803), Expect = 7e-90 Identities = 184/501 (36%), Positives = 283/501 (56%), Gaps = 14/501 (2%) Query: 6 YLSQGFAVAMTPENLVIALIGCFVGTIVGLLPGLGPINGVAILLPLAFALHLPAESALIL 65 + Q +P + + +IG G I G +PG + ++ P FA+ S + L Sbjct: 4 FFLQALGQVGSPSVVALIVIGVLFGIIGGSIPGFTVTMAILVVFPFTFAMD--PVSGVSL 61 Query: 66 LATVYIGCEYGGRISSILLNVPGDAAAIMTALDGYPMAQQGKGGVALSISAVSSFFGSLI 125 + V++G GG +S ++L +PG ++I T DGYPMAQ G+ G AL I +SF G+LI Sbjct: 62 MVGVFVGGYSGGIVSGVMLGIPGTPSSITTVYDGYPMAQNGEPGRALGIGVAASFLGTLI 121 Query: 126 AIGGIILFAPLLAQWSLAFGPAEYFALMVFAIACLGSMMAQNPLKSFLAALIGLGLATVG 185 ++ ++ F PL+A +S+ F P E AL+VFA+ + + LK LAA +GL + TVG Sbjct: 122 SVAVLVFFGPLIAGFSMNFRPWEITALIVFALTLVAGLSNGALLKGLLAAALGLLITTVG 181 Query: 186 VDANTGVYRFTFDSVHLSDGVQFIVVVIGLFSVSEILLMLEHTSSGQTMVRKT------- 238 D N+ + RF F L G + + V+IGLF+ S+++ LE + V+ Sbjct: 182 YDRNSNL-RFDFGIPALGSGFEILPVMIGLFAFSQLMENLEKLRDEKDKVKGVDTNVAIP 240 Query: 239 -GRMLFNLKEGAQCIGTTLRSSVIGFFVGVLPGAGATIASAITYMTEKKLSGNSDSFGKG 297 GR+L K+ A TLRSS+IG +G LPG G T+A+ ++Y KK S ++FGKG Sbjct: 241 YGRIL---KDMAGQKLNTLRSSLIGSLIGALPGTGGTVANFLSYDQAKKFSRQPETFGKG 297 Query: 298 DIRGVAAPEAANNASACGSFIPMLTLGVPGSGTTAVMMGALTLYNITPGPAMFTEQPDIV 357 G+ A EA+N+A A G+F+P L LG+PG A+MMG L L+ ITPGP MF + P +V Sbjct: 298 TPSGIVASEASNSAVAGGAFVPTLALGIPGDLPMAIMMGVLILHGITPGPLMFEQNPVLV 357 Query: 358 WGLIAALLIANVMLLIMNIPLIGLFTRMLTIPLWFVVPAIAAVSAVGVYAVHSTTFDLVL 417 + A+LLI V++++ + L+ F ++ IP +VP + + A+G YA+++ FD+ + Sbjct: 358 GAIYASLLIGAVVMVLCQLLLVRWFAKISLIPQEILVPVVLMLCAIGSYALNNNLFDIWV 417 Query: 418 MVALGVLGYILRKMHFPMSPLILGFVLGEMLEQNLRRALSISNGNMAILWQSGVAKALLI 477 + GV+GY+L K P++PLILG VLG LE+ L RAL + + M L + A L + Sbjct: 418 LFIFGVIGYLLWKAEVPLTPLILGVVLGNNLERQLFRALELDDSWMTFLTRPLSALFLAL 477 Query: 478 MAIMVIVVPPVLRLLRKHSRK 498 VI R +R++ K Sbjct: 478 AVASVIFSLYQDRKIRRNRHK 498 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: 773 Number of extensions: 51 Number of successful extensions: 6 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: 504 Length adjustment: 34 Effective length of query: 470 Effective length of database: 470 Effective search space: 220900 Effective search space used: 220900 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 24 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