Align Tricarboxylic transport TctA (characterized, see rationale)
to candidate 3609059 Dshi_2448 protein of unknown function DUF112 transmembrane (RefSeq)
Query= uniprot:E4PJQ9 (508 letters) >FitnessBrowser__Dino:3609059 Length = 498 Score = 344 bits (882), Expect = 5e-99 Identities = 182/476 (38%), Positives = 282/476 (59%), Gaps = 5/476 (1%) Query: 14 ALTPYNLMFALFGAFVG-TLIGCLPGLGPANGVAILIPLAFTLGLPPETAMILLTAVYAG 72 AL +L+ LF A +G +IG LPGL G A+L+P FT+ + P A+ +LT +Y Sbjct: 10 ALMDPSLLVLLFAATLGGVIIGALPGLNATTGAALLLP--FTITMDPIPAIAILTTIYCA 67 Query: 73 AMYGGRISSILLNIPGDEPAMMTCLDGYPMAQKGRAADALAVSAIASFAGGLIGTIGLIM 132 A + G I++IL+N PG + TCLDGYP+AQ+G A AL ++ ++S GG+I + L+M Sbjct: 68 ATFAGAITAILINTPGTSASATTCLDGYPLAQRGEAGRALGMATVSSTIGGIISVVCLMM 127 Query: 133 LAPVLAKFALTFGPAEYFALFLLAFATLGGITGKNPVKTVVAATLGIMISTVGIDISTGT 192 AP++A+ A F P EYFAL + + L I P+K ++A LG+ ++TVG D+ T Sbjct: 128 AAPLMARMAYNFAPPEYFALTVFGISMLATIGDGTPLKNIIAGALGVFLATVGKDLLTTV 187 Query: 193 QRYTFGVLELYEGIDFILAIVGLFAISELLFFVESRMGRGRDKMNVGKLTLTMKELVMTI 252 +R+TFG EL EGI F+ ++G+F ISELL E R+ R + + + L +E + Sbjct: 188 ERFTFGFNELSEGIGFVPVMIGIFGISELLVQAE-RLQAKRKLIEMKAIKLPSREDYRKV 246 Query: 253 -PTQLRGGVLGFISGVLPGAGASLGSFISYTLEKQVVGKKGKFGEGDIRGVVAPEAGNNG 311 T LR +G G+LP GA++ S I Y ++ +FG+G I G+ EA NN Sbjct: 247 WRTILRSSGIGTFIGILPAEGATVASMIGYNEARRWSKTPEEFGKGAIEGIAGSEAANNS 306 Query: 312 ASSGALVPMLTLGVPGSGTTAVLLAMLISLNITPGPLMFTQNADIVWGVIAALLIGNVLL 371 A+ GA+VP L LG+PGS T AV+LA L+ + PGP MFT+ A+ + + A+L+ NV Sbjct: 307 ATGGAMVPTLALGIPGSPTAAVILAGLMVHGLQPGPTMFTEQAEFAYAIFWAMLLVNVTF 366 Query: 372 LVLNIPLVGFFVKLLSVPPMYLLPIVTMVAFVGIYSISHSTFDLYFMVAFGVAGYFLRKL 431 + + + F ++ VP L P+V + VG Y++ S D+Y +A GV GYF+R+ Sbjct: 367 IFVGLFGAKLFARVTFVPVQILWPVVFTFSIVGAYALDQSMLDVYIALASGVVGYFMRRF 426 Query: 432 EIPLVPIILGLLLGPEMEKNLGHALVLSDGEWSVLWASPLAMGLWIVAGLGLILPY 487 +VP+ +GL+LG +EK LG +L++ D +W +++ PL + +++ L L P+ Sbjct: 427 GYSVVPLAIGLILGGMLEKRLGQSLIMLDDQWWLMFTRPLTLFFFVLTVLALFGPF 482 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: 721 Number of extensions: 41 Number of successful extensions: 3 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: 498 Length adjustment: 34 Effective length of query: 474 Effective length of database: 464 Effective search space: 219936 Effective search space used: 219936 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