Align Tricarboxylic transport TctA (characterized, see rationale)
to candidate WP_005813871.1 DHAF_RS09820 hypothetical protein
Query= uniprot:E4PJQ9 (508 letters) >NCBI__GCF_000021925.1:WP_005813871.1 Length = 503 Score = 444 bits (1142), Expect = e-129 Identities = 227/495 (45%), Positives = 327/495 (66%), Gaps = 14/495 (2%) Query: 1 METLGFLMDGFAVALTPYNLMFALFGAFVGTLIGCLPGLGPANGVAILIPLAFTLGLPPE 60 METL L G +VA P NL++ + G G +IG LPGLGP+ G+AIL+PL F G P Sbjct: 1 METLQNLAMGLSVATDPMNLLYCVIGVMFGIVIGALPGLGPSAGIAILLPLTF--GTDPV 58 Query: 61 TAMILLTAVYAGAMYGGRISSILLNIPGDEPAMMTCLDGYPMAQKGRAADALAVSAIASF 120 +I+L +Y GAMYGG I+SIL+N PGD A+MT LDG+P+A++GRA AL ++A AS Sbjct: 59 AGIIMLAGIYYGAMYGGSITSILINTPGDASAVMTTLDGHPLAKQGRAGQALGMAAFASI 118 Query: 121 AGGLIGTIGLIMLAPVLAKFALTFGPAEYFALFLLAFATLGGITGKNPVKTVVAATLGIM 180 GG + + + LAP LA+FA+TFGP EYFAL +L T+GG+TGK P K ++A +G+ Sbjct: 119 IGGTVCVVLFMFLAPALAEFAITFGPPEYFALMVLGLTTIGGMTGKFPAKGYMSALVGLF 178 Query: 181 ISTVGIDISTGTQRYTFGVLELYEGIDFILAIVGLFAISELLFFVESRMGRGRDKMNVGK 240 I+T+G+D+ G R+TFG ELYEGIDFI +GLF I+ELL E G +K+ V K Sbjct: 179 IATIGLDLVQGIPRFTFGAYELYEGIDFIPVAMGLFGIAELLVISE-----GGEKIKVSK 233 Query: 241 LTLTMKELVMTI-------PTQLRGGVLGFISGVLPGAGASLGSFISYTLEKQVVGKKGK 293 LT ++ + P RG +GF G+LPGAGA++ SFISY + +++ + K Sbjct: 234 KDLTWRKQLPNKEDWKYAGPHIARGTGIGFFIGMLPGAGATIASFISYGIARKISKRGDK 293 Query: 294 FGEGDIRGVVAPEAGNNGASSGALVPMLTLGVPGSGTTAVLLAMLISLNITPGPLMFTQN 353 FG G I GV APE+ NN AS GA+VP+LTLGVPGSG+TAV++ L+ +TPGPL+F N Sbjct: 294 FGTGVIEGVAAPESANNAASMGAMVPLLTLGVPGSGSTAVMMGALMMFGLTPGPLLFENN 353 Query: 354 ADIVWGVIAALLIGNVLLLVLNIPLVGFFVKLLSVPPMYLLPIVTMVAFVGIYSISHSTF 413 D VWG+I ++ IGN LLL+ + V FVK+L+V L +V +G YS+++S F Sbjct: 354 PDFVWGLIGSMYIGNFLLLIAAMLCVPLFVKVLNVSSPILNAVVMAFILIGAYSLNNSMF 413 Query: 414 DLYFMVAFGVAGYFLRKLEIPLVPIILGLLLGPEMEKNLGHALVLSDGEWSVLWASPLAM 473 D+ + FG+ G+F++KLE P P++L L+LG +E +L +L++S+G +V + P++ Sbjct: 414 DVGLTILFGILGFFMKKLEFPATPMVLALVLGALLETSLRQSLIISNGNPAVFFTRPISG 473 Query: 474 GLWIVAGLGLILPYL 488 + +++ L +I P++ Sbjct: 474 TILVISILAIIWPFI 488 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: 845 Number of extensions: 55 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: 503 Length adjustment: 34 Effective length of query: 474 Effective length of database: 469 Effective search space: 222306 Effective search space used: 222306 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