Align Tricarboxylic transport TctA (characterized, see rationale)
to candidate 3610834 Dshi_4220 protein of unknown function DUF112 transmembrane (RefSeq)
Query= uniprot:E4PJQ9 (508 letters) >FitnessBrowser__Dino:3610834 Length = 494 Score = 332 bits (851), Expect = 2e-95 Identities = 184/491 (37%), Positives = 282/491 (57%), Gaps = 18/491 (3%) Query: 7 LMDGFAVALTPYNLMFALFGAFVGTLIGCLPGLGPANGVAILIPLAFTLGLPPETAMILL 66 L FA+ L+P L+ G +G ++G LPG+G VA+++P FTL + A++LL Sbjct: 5 LPQAFALLLSPQGLLVLSVGTMLGIVLGALPGIGSTVAVAMILP--FTLTMDQAPAILLL 62 Query: 67 TAVYAGAMYGGRISSILLNIPGDEPAMMTCLDGYPMAQKGRAADALAVSAIASFAGGLIG 126 A+YAG++YGG IS+IL+N PG + TCLDG+PMAQ+G A AL + IAS GGL Sbjct: 63 LAIYAGSVYGGSISAILINTPGTPQSAATCLDGFPMAQRGEAGKALGWATIASVVGGLTS 122 Query: 127 TIGLIMLAPVLAKFALTFGPAEYFALFLLAFATLGGITGKNPVKTVVAATLGIMISTVGI 186 + LI AP LA FAL FGP E FAL LL + ++ + VK ++A LGI +STVG Sbjct: 123 AVVLIFAAPQLAAFALNFGPIETFALILLGLTCIVSVSEGSLVKGLMAGMLGIFLSTVGG 182 Query: 187 DISTGTQRYTFGVLELYEGIDFILAIVGLFAISELLFFVESRMGRGRDKMNVGKLTLTMK 246 D TG R+TFG +L G + + ++G+FA+SE+L R G D V + K Sbjct: 183 DPITGEARFTFGQFQLIAGFNLLAVVIGVFALSEVLI----RASSGPDSTGV---LVDFK 235 Query: 247 ELVMTIPTQLRGGVLGFIS--------GVLPGAGASLGSFISYTLEKQVVGKKGKFGEGD 298 +V+ + +G + G G+LPG GA+ +FISY ++ + FG+G+ Sbjct: 236 GIVLPRWAEWKGRLRGLAKSVAIGNGVGILPGTGAATAAFISYAEARRSAPTRANFGKGE 295 Query: 299 IRGVVAPEAGNNGASSGALVPMLTLGVPGSGTTAVLLAMLISLNITPGPLMFTQNADIVW 358 G++A E+ NN + GALVP + LG+PG TAV+LA L +TPG + N ++ Sbjct: 296 PDGLIASESANNAVTGGALVPTMALGIPGDAITAVMLATLTLHGVTPGIRLMQDNPVLMA 355 Query: 359 GVIAALLIGNVLLLVLNIPLVGFFVKLLSVPPMYLLPIVTMVAFVGIYSISHSTFDLYFM 418 + A I N++LL L + + LL + Y+L ++T++ VG++ + + FDL M Sbjct: 356 SIFAGFFIINLMLLPLGMLVSKLAAPLLRMREAYMLIVITLLCTVGVFFVRGNPFDLLVM 415 Query: 419 VAFGVAGYFLRKLEIPLVPIILGLLLGPEMEKNLGHALVLSDGEWSVLWAS-PLAMGLWI 477 G+ G+ LR+ P+ P+++G++LGP +E +L L+++DG + + P+A+GL I Sbjct: 416 AGAGIVGFVLRRQGYPMAPLVIGMVLGPTLELSLRQGLIITDGNFGAFFTGHPIALGLTI 475 Query: 478 VAGLGLILPYL 488 A L LP + Sbjct: 476 AAAGMLSLPLI 486 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: 779 Number of extensions: 50 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 508 Length of database: 494 Length adjustment: 34 Effective length of query: 474 Effective length of database: 460 Effective search space: 218040 Effective search space used: 218040 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