Align Tricarboxylic transport TctA (characterized, see rationale)
to candidate 3607810 Dshi_1218 protein of unknown function DUF112 transmembrane (RefSeq)
Query= uniprot:E4PJQ9 (508 letters) >FitnessBrowser__Dino:3607810 Length = 504 Score = 394 bits (1012), Expect = e-114 Identities = 210/494 (42%), Positives = 302/494 (61%), Gaps = 10/494 (2%) Query: 1 METLGFLMDGFAVALTPYNLMFALFGAFVGTLIGCLPGLGPANGVAILIPLAFTLGLPPE 60 M+ L +GFA +L+P N+ L G VG IG +PGLG NGVAI++PL F + PP Sbjct: 1 MDIFPLLAEGFATSLSPLNIFIVLIGVTVGLFIGAMPGLGSVNGVAIVLPLTFVV--PPA 58 Query: 61 TAMILLTAVYAGAMYGGRISSILLNIPGDEPAMMTCLDGYPMAQKGRAADALAVSAIASF 120 +A+ILL A+Y GAMYGG +SSILL IPG A+ T DG PMAQKG A AL +A+ASF Sbjct: 59 SAIILLCAIYYGAMYGGAVSSILLGIPGASTAVATTFDGRPMAQKGEAGLALIAAAVASF 118 Query: 121 AGGLIGTIGLIMLAPVLAKFALTFGPAEYFALFLLAFATLGGITGKNPVKTVVAATLGIM 180 GG I I A LA AL FGPAE FAL LLAF T G+ G + +KT+V LG++ Sbjct: 119 IGGTISVILFTAFAIPLADLALAFGPAEEFALVLLAFTTFVGLGGDDALKTIVMICLGLV 178 Query: 181 ISTVGIDISTGTQRYTFGVLE-LYEGIDFILAIVGLFAISELLFFVESRMGRGRDKMNVG 239 +STVG+D+ +G R FG L Y GI F++ +G++ I E+L+ +E+ + + Sbjct: 179 LSTVGLDLISGQPRLIFGDLPGFYSGISFLVLAIGVYGIGEILYTIET--SKKSPTVTAA 236 Query: 240 KLTLT-----MKELVMTIPTQLRGGVLGFISGVLPGAGASLGSFISYTLEKQVVGKKGKF 294 K+T + ++ + T G LGF G+LP AGA+ + ++Y + + K F Sbjct: 237 KITFSELGAGLRRMNKLWKTMSMGSFLGFFVGMLPAAGATPAALMAYGIARTTSKKSENF 296 Query: 295 GEGDIRGVVAPEAGNNGASSGALVPMLTLGVPGSGTTAVLLAMLISLNITPGPLMFTQNA 354 G+G+I GV APE NN AS+G+L+PMLTLG+PGS TTA+LL ++ + PGP++F + Sbjct: 297 GKGEIEGVAAPETANNAASTGSLLPMLTLGIPGSPTTALLLGGMVMWGLVPGPMLFIEQP 356 Query: 355 DIVWGVIAALLIGNVLLLVLNIPLVGFFVKLLSVPPMYLLPIVTMVAFVGIYSISHSTFD 414 D VWG+I++L NV +++N+ L+ FV L +P L +V ++ VG ++ S D Sbjct: 357 DFVWGMISSLYTANVAAVLINLALIPLFVWALRMPFTVLCSVVVVLCIVGGFAPSQKIHD 416 Query: 415 LYFMVAFGVAGYFLRKLEIPLVPIILGLLLGPEMEKNLGHALVLSDGEWSVLWASPLAMG 474 ++ + AFG+ GY LRK + PL P++L L+LGP MEK+ +LV+ G V PL+ Sbjct: 417 VWLIAAFGILGYILRKADYPLAPLVLALVLGPLMEKSFRQSLVMEQGNVFVFVERPLSAT 476 Query: 475 LWIVAGLGLILPYL 488 ++A + +LP L Sbjct: 477 FMVLALIFFLLPLL 490 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: 801 Number of extensions: 40 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: 508 Length of database: 504 Length adjustment: 34 Effective length of query: 474 Effective length of database: 470 Effective search space: 222780 Effective search space used: 222780 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 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