Align Tricarboxylic transport TctA (characterized, see rationale)
to candidate GFF3175 PGA1_c32260 putative integral membrane protein
Query= uniprot:E4PJQ9 (508 letters) >FitnessBrowser__Phaeo:GFF3175 Length = 505 Score = 291 bits (746), Expect = 3e-83 Identities = 157/433 (36%), Positives = 245/433 (56%), Gaps = 2/433 (0%) Query: 24 LFGAFVGTLIGCLPGLGPANGVAILIPLAFTLGLPPETAMILLTAVYAGAMYGGRISSIL 83 L G+ G +IG +PG+GPA +AIL+P F P + +L +Y +MYGG I ++L Sbjct: 21 LIGSIGGVVIGAIPGVGPAVAIAILLPATFAFD--PIVGLTMLLGIYGSSMYGGAIPAVL 78 Query: 84 LNIPGDEPAMMTCLDGYPMAQKGRAADALAVSAIASFAGGLIGTIGLIMLAPVLAKFALT 143 +N PG +T DG+PM QKG A AL+++ ASF GG+ G LI+L+PVLA A Sbjct: 79 INTPGTAVNALTSYDGHPMTQKGDAHRALSLAYSASFWGGIFGIGCLILLSPVLALVAPM 138 Query: 144 FGPAEYFALFLLAFATLGGITGKNPVKTVVAATLGIMISTVGIDISTGTQRYTFGVLELY 203 FG E F LL + V A GI + T+G+D T TQRYTFG+ L Sbjct: 139 FGSREIFLAALLGVVLVILAHRGQIFAAGVLAMFGIFLQTIGLDAVTYTQRYTFGLTFLS 198 Query: 204 EGIDFILAIVGLFAISELLFFVESRMGRGRDKMNVGKLTLTMKELVMTIPTQLRGGVLGF 263 G++ I+ ++GLFA+S+ F + + K G+++ ++EL+ G Sbjct: 199 SGVNLIVVVLGLFALSQAFFLLTTPDNSPDAKPVSGRMSAGIRELMRHKRVATVASGCGV 258 Query: 264 ISGVLPGAGASLGSFISYTLEKQVVGKKGKFGEGDIRGVVAPEAGNNGASSGALVPMLTL 323 I G++PG G F+SYT ++ FG+G G++A EA NN + A++P+L L Sbjct: 259 ILGMIPGTGEFTAQFMSYTYAQKTSKTPDLFGKGSPEGLIASEAANNAVPAAAMIPLLAL 318 Query: 324 GVPGSGTTAVLLAMLISLNITPGPLMFTQNADIVWGVIAALLIGNVLLLVLNIPLVGFFV 383 G+PG TA++L++ N+ PGP +F N D+V+G+ AL++ NV+++ + Sbjct: 319 GIPGEALTAMMLSVFYVHNVIPGPQLFQNNIDLVYGLYLALILLNVIVVAFLMVSTNLLT 378 Query: 384 KLLSVPPMYLLPIVTMVAFVGIYSISHSTFDLYFMVAFGVAGYFLRKLEIPLVPIILGLL 443 +++ +P +L ++ +++FVG+YS+ +S D FGV G L++L +P+VPIILG++ Sbjct: 379 RIIRIPTRFLGVLILLLSFVGVYSLRNSLTDCMIAAGFGVLGLILKRLNLPIVPIILGMV 438 Query: 444 LGPEMEKNLGHAL 456 LG ME L AL Sbjct: 439 LGGIMEVKLRSAL 451 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: 730 Number of extensions: 43 Number of successful extensions: 4 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: 505 Length adjustment: 34 Effective length of query: 474 Effective length of database: 471 Effective search space: 223254 Effective search space used: 223254 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