Align Tricarboxylic transport TctA (characterized, see rationale)
to candidate WP_015942890.1 DHAF_RS03160 hypothetical protein
Query= uniprot:E4PJQ9 (508 letters) >NCBI__GCF_000021925.1:WP_015942890.1 Length = 502 Score = 418 bits (1074), Expect = e-121 Identities = 219/509 (43%), Positives = 315/509 (61%), Gaps = 17/509 (3%) Query: 1 METLGFLMDGFAVALTPYNLMFALFGAFVGTLIGCLPGLGPANGVAILIPLAFTLGLPPE 60 ME L L GFA+AL P N++ A GAFVGT++G LPGLGP + +AIL+PL T LPP Sbjct: 1 MEALQMLFSGFALALEPSNILMAALGAFVGTMVGVLPGLGPTSAIAILLPL--TAVLPPT 58 Query: 61 TAMILLTAVYAGAMYGGRISSILLNIPGDEPAMMTCLDGYPMAQKGRAADALAVSAIASF 120 A+I+L +Y GAMYGG ++ILLNIPG+ ++ TCLDGYPMAQ+GR AL ++AI SF Sbjct: 59 QAIIMLAGIYYGAMYGGSSTAILLNIPGEVASVPTCLDGYPMAQQGRGGPALGIAAIGSF 118 Query: 121 AGGLIGTIGLIMLAPVLAKFALTFGPAEYFALFLLAFATLGGITGKNPVKTVVAATLGIM 180 G++G I L AP+ A+ AL FGP EYFAL LLA + + G + K + G + Sbjct: 119 IAGIMGIIALTFFAPLFAEQALKFGPPEYFALMLLALTIVVSLGGASIGKALAMGFFGYL 178 Query: 181 ISTVGIDISTGTQRYTFGVLELYEGIDFILAIVGLFAISELLFFVESR-----MGRGRDK 235 +S +G+ T R TFG L+ G+D I ++GLFAISE+L +E + MG Sbjct: 179 LSLIGLGTMTNMPRLTFGYTPLWGGLDVISVVIGLFAISEVLNGIEEKKIAISMG----- 233 Query: 236 MNVGKLTLTMKELVMTIPTQLRGGVLGFISGVLPGAGASLGSFISYTLEKQVVGKKGKFG 295 N+G + +K+L +I + RGG LGF G+LPG ++ +F++Y LEK+ +FG Sbjct: 234 -NIGSVFPGLKDLKQSIKSIFRGGALGFFMGLLPGCSPAVTTFLAYDLEKKCSKTPERFG 292 Query: 296 EGDIRGVVAPEAGNNGASSGALVPMLTLGVPGSGTTAVLLAMLISLNITPGPLMFTQNAD 355 +G I GV APE+ NN SS +P+ LG+P S AVLL L+ +TPGPL+F QN D Sbjct: 293 KGAIEGVAAPESANNATSSAGFIPLFALGIPASPPLAVLLGGLMIYGLTPGPLLFEQNGD 352 Query: 356 IVWGVIAALLIGNVLLLVLNIPLVGFFVKLLSVPPMYLLPIVTMVAFVGIYSISHSTFDL 415 VW VIA++ IGNV+ LVLN+PLVG + +L +P L PI+ +++ VG Y++ + FD+ Sbjct: 353 FVWAVIASMFIGNVMCLVLNLPLVGLWARLTQIPYGILAPIILLISIVGAYTVRNDMFDV 412 Query: 416 YFMVAFGVAGYFLRKLEIPLVPIILGLLLGPEMEKNLGHALVLSDGEWSVLWASPLAMGL 475 + FGV GYF+ K P+VP I+ +LGP +E++L + ++ + + P+++ L Sbjct: 413 LVALIFGVVGYFMNKFNWPVVPFIICFILGPMLERSLLQSFGMAFENPFIFFQRPISLTL 472 Query: 476 WIVAGLGLILPYLVGPLLRRRMNAAMKES 504 + G+ L+ V LRRR + + S Sbjct: 473 LVATGIFLV----VSLKLRRRTQSRIDNS 497 Lambda K H 0.325 0.144 0.425 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: 827 Number of extensions: 51 Number of successful extensions: 5 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: 508 Length of database: 502 Length adjustment: 34 Effective length of query: 474 Effective length of database: 468 Effective search space: 221832 Effective search space used: 221832 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 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