Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate AZOBR_RS30120 AZOBR_RS30120 C4-dicarboxylate ABC transporter permease
Query= reanno::PV4:5208943 (465 letters) >FitnessBrowser__azobra:AZOBR_RS30120 Length = 427 Score = 255 bits (652), Expect = 2e-72 Identities = 151/461 (32%), Positives = 247/461 (53%), Gaps = 38/461 (8%) Query: 1 MTIATLFISLFLCMLLGMPIAIALGFSSMLTILLFSDDSLASVALKLYESTSEHYTLLAI 60 M + L ++ F ++LG+P+A A+G S++ TIL + +V + S ++ LAI Sbjct: 1 MELTILAVTFFGFLVLGIPVAFAIGLSALCTILY--EGLPVAVIFQQMMSGMNVFSFLAI 58 Query: 61 PFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIG 120 PFF+ S + GGVA +I+ A + VGHIRGGL M++V+AC LF V+GS A V+A+G Sbjct: 59 PFFVFSGELMLHGGVADKIVATAKNMVGHIRGGLGMSNVVACTLFGGVAGSPVADVSAMG 118 Query: 121 SIVIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAAT--EVSAARMFMAGLIP 178 +++I M R GY +A V T + +G L+P S M++YA A + S + AG++P Sbjct: 119 AVMIPMMKREGYHADYAVNVTTHAALVGALMPTSHNMIIYALAAGGKASIGALIAAGIVP 178 Query: 179 GLMMGLLLMLAIYIVARIKKLPSRPFPGFRPLAISSAKAMGGLALIVIVLGSIYGGIASP 238 L++ + + A Y VA + P FPG+ L S A A GL ++VI+L I G+ + Sbjct: 179 ALLLMVCNLGAAYYVAVKRGYPPGTFPGWSILGRSFAAAAPGLLIVVIILAGITSGVFTA 238 Query: 239 TEAAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPADKE 298 TE+A++A +YA + F YR ++W + A KT Sbjct: 239 TESASIAVIYALLLTTFVYR------TLTW---------------DHFLAAAAKT----- 272 Query: 299 IRHVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLIIVNLLL 358 K + ++L +I + +F +++ ++ + E + G+ +++N++L Sbjct: 273 --------VKTTGVVLLLIGVSTMFQYIMGLYQVAEITGELMAGISTNPLVIFLLINIIL 324 Query: 359 LAAGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAG 418 G FM+ ++ +LI PI PIA Q G+DP+ GI+M++N +G+ TPPVG F+ Sbjct: 325 FLLGTFMDMASTILICTPIFLPIAMQYGMDPVQFGIVMLINCALGLNTPPVGTTQFIGCA 384 Query: 419 ITGRSMGWVIHSCIPWLALLLFFLALITYIPQISLFLPEYI 459 I S+G V+ S P+ L L L+TY+P SL+LP + Sbjct: 385 IGEVSVGQVMRSITPFYGALFVTLLLVTYVPTFSLWLPHML 425 Lambda K H 0.330 0.144 0.424 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: 538 Number of extensions: 27 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: 465 Length of database: 427 Length adjustment: 32 Effective length of query: 433 Effective length of database: 395 Effective search space: 171035 Effective search space used: 171035 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 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