Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate GFF3978 HP15_3918 trap-type mannitol/chloroaromatic compound transport system, large permease component
Query= reanno::PV4:5208943 (465 letters) >FitnessBrowser__Marino:GFF3978 Length = 436 Score = 224 bits (570), Expect = 6e-63 Identities = 160/465 (34%), Positives = 242/465 (52%), Gaps = 52/465 (11%) Query: 7 FISLFLCMLLGMPIAIALGFSSMLTILL-FSDDSLASVALKLYESTSEHYTLLAIPFFIL 65 F SL +LLG+P+A LG S++ + + DS VA +++ T +TL+AIP F+ Sbjct: 11 FGSLLFFLLLGLPLAFVLGGVSVVFLYFTWGFDSFYMVASQIW-GTMGSFTLVAIPLFVF 69 Query: 66 SSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGSIVIV 125 + L GVAR + G +RGGLA+ ++ C +FAA+ G S A V A+G+I + Sbjct: 70 MAMILERTGVARDLYRMMHLWCGGLRGGLALGTLGICAVFAAMVGISGAAVVAMGTIALP 129 Query: 126 GMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGLMMGLL 185 M+ GY + A GVI T G GILIPPSI+M++YA T VS +MF AG++PG++ L+ Sbjct: 130 SMLERGYDKSMALGVINTGGGWGILIPPSILMILYALITGVSVGKMFAAGIMPGVL--LM 187 Query: 186 LMLAIYIVARIKKLPS------RPFPGFRPLAISSAKA-MGGLALIVIVLGSIYGGIASP 238 ++ AIYI+ R P + G P + +A + + ++V+VLGSI GGI +P Sbjct: 188 VLTAIYIIVRCHLQPELAPALPKEDRGTWPEKFRALRAVLLPIGVVVMVLGSIIGGITTP 247 Query: 239 TEAAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPADKE 298 TEAAA+ V I+ YR W E IR Sbjct: 248 TEAAAMG-VLGALISAAVYRQF------KWSILKEAAIRTF------------------- 281 Query: 299 IRHVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGM--GLPVWGFLIIVNL 356 K++ M+++I+ A F+ + LI E ++ M G P WG +I + + Sbjct: 282 ---------KLTGMIMWILFAAHAFSAAYQSMGAQELI-EGLMNMVPGGP-WGIIIAMMV 330 Query: 357 LLLAAGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVT 416 ++ ++P I+LI P+ PI LG DPI GI+ V+NMEIG +TPP G NLF Sbjct: 331 IVFLLAMVLDPVGIMLITLPVFMPIVESLGFDPIWFGILFVINMEIGYMTPPFGFNLFYL 390 Query: 417 AGITGRS--MGWVIHSCIPWLALLLFFLALITYIPQISLFLPEYI 459 GI S M + S IP++ + + + LI P+I+ +LP+ + Sbjct: 391 KGIVPPSITMKDIYKSIIPFVIVEIVGIILIMVFPEIATWLPDLL 435 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: 650 Number of extensions: 36 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: 2 Length of query: 465 Length of database: 436 Length adjustment: 33 Effective length of query: 432 Effective length of database: 403 Effective search space: 174096 Effective search space used: 174096 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