Align neutral amino acid transporter B(0) (characterized)
to candidate GFF4198 PS417_21500 C4-dicarboxylate transporter
Query= CharProtDB::CH_091706 (553 letters) >FitnessBrowser__WCS417:GFF4198 Length = 443 Score = 147 bits (372), Expect = 6e-40 Identities = 127/473 (26%), Positives = 218/473 (46%), Gaps = 82/473 (17%) Query: 53 LVLLTVAAVVAGVGLGLGVSAAGGADALGPARLTRFAFPGELLLRLLKMIILPLVVCSLI 112 L + A+V G+ LG G A L P G+ ++L+KM+I P++ C+++ Sbjct: 11 LYFQVIVAIVIGILLGHFYPQTGVA--LKPL--------GDGFIKLIKMVIAPIIFCTVV 60 Query: 113 GGAASLDP-SALGRVGAWALLFFLVTTLLASALGVGLALALKPGAAVTAITSINDSVVDP 171 G A + ++G+ G +ALL+F + + +A +G+ + ++PG + I+ + +D Sbjct: 61 SGIAGMQSMKSVGKTGGYALLYFEIVSTVALLIGLIVVNVVQPGNGM----HIDVATLDA 116 Query: 172 CARSAPTKEALD-SFLDLVRNIFPSNLVSAAFRSFATSYEPKDNSCKIPQSCIQREINST 230 +A D S + + N+ P+ +V A FA Sbjct: 117 SKVAAYVTAGKDQSIVGFILNVIPNTIVGA----FANG---------------------- 150 Query: 231 MVQLLCEVEGMNILGLVVFAIVFGVALRKLGPEGELLIRFFNSFNDATMVLVSWIMWYAP 290 +IL +++F+++FG AL +LG G+ ++ F + F +++ IM AP Sbjct: 151 -----------DILQVLMFSVIFGFALHRLGAYGKPVLDFIDRFAHVMFNIINMIMKLAP 199 Query: 291 VGILFLVASKIVEMKDVRQLFISLGKYILC----CLLGHAI--------HGLLVLPLIYF 338 +G L +A I V L + LG+ ++C CLL + HG V+ LI + Sbjct: 200 IGALGAMAFTIGAY-GVGSL-VQLGQLMICFYITCLLFVLVVLGGICRAHGFSVIKLIRY 257 Query: 339 LFTRKNPYRFLWGIMTPLATAFGTSSSSATLPLMMKCVEEKNGVAKHISRFILPIGATVN 398 I L GTSSS + LP M+ +E + G K + ++P G + N Sbjct: 258 -------------IREELLIVLGTSSSESALPRMLIKME-RLGAKKSVVGLVIPTGYSFN 303 Query: 399 MDGAALFQCVAAVFIAQLNGVSLDFVKIITILVTATASSVGAAGIPAGGVLTLAIILEAV 458 +DG +++ +AAVFIAQ +D IT+L+ SS GAAG+ G + LA L AV Sbjct: 304 LDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAV 363 Query: 459 S-LPVKDISLILAVDWLVDRSCTVLNVEGDAFGAGLLQSYVDRTKMPSSEPEL 510 LPV ++LIL +D + + + N+ G+A ++ +V + EL Sbjct: 364 GHLPVAGLALILGIDRFMSEARALTNLVGNAVATIVVAKWVKELDTDKLQSEL 416 Lambda K H 0.323 0.138 0.406 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: 427 Number of extensions: 21 Number of successful extensions: 3 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: 553 Length of database: 443 Length adjustment: 34 Effective length of query: 519 Effective length of database: 409 Effective search space: 212271 Effective search space used: 212271 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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