Align D-gluconate TRAP transporter, large permease component (characterized)
to candidate GFF3978 HP15_3918 trap-type mannitol/chloroaromatic compound transport system, large permease component
Query= reanno::psRCH2:GFF2081 (425 letters) >FitnessBrowser__Marino:GFF3978 Length = 436 Score = 214 bits (544), Expect = 5e-60 Identities = 130/426 (30%), Positives = 232/426 (54%), Gaps = 15/426 (3%) Query: 4 VVFLSSLLGFMTLGMPIAFALLLTGSVLMWYL-DFWDVQLLAQNLQAGADSFPLLAVPFF 62 ++F SLL F+ LG+P+AF L V +++ F ++A + SF L+A+P F Sbjct: 8 LLFFGSLLFFLLLGLPLAFVLGGVSVVFLYFTWGFDSFYMVASQIWGTMGSFTLVAIPLF 67 Query: 63 ILAGELMNAGGISRRIIAMAQAYFGHKRGGLGYVAIAASVLLASMSGSALADTAALATLL 122 + ++ G++R + M + G RGGL + + A+M G + A A+ T+ Sbjct: 68 VFMAMILERTGVARDLYRMMHLWCGGLRGGLALGTLGICAVFAAMVGISGAAVVAMGTIA 127 Query: 123 LPMMRERGYPLSSSSGLVAAGGIIAPIIPPSMPFVIYGVVTGTSISQLFLAGMVPGLIMG 182 LP M ERGY S + G++ GG +IPPS+ ++Y ++TG S+ ++F AG++PG+++ Sbjct: 128 LPSMLERGYDKSMALGVINTGGGWGILIPPSILMILYALITGVSVGKMFAAGIMPGVLL- 186 Query: 183 MGLIVAWTLIARRIDE------PKQEKASAAERRRVLVDGAAALMLPVIIVGGLRGGLFT 236 M L + ++ + PK+++ + E+ R L + + V+++G + GG+ T Sbjct: 187 MVLTAIYIIVRCHLQPELAPALPKEDRGTWPEKFRALRAVLLPIGVVVMVLGSIIGGITT 246 Query: 237 PTEAAVVAAVYALAVSTLLYRELNWAGLVEVLTRASRTTASVMFLCAAATV--SAYMITL 294 PTEAA + + AL +S +YR+ W+ L E R + T +M++ AA +AY Sbjct: 247 PTEAAAMGVLGAL-ISAAVYRQFKWSILKEAAIRTFKLTGMIMWILFAAHAFSAAYQSMG 305 Query: 295 AQLPDEIAAMLGPLAQDPKLLMVAIMLLMIAVGMVLDLTPTILILGPVLAPIAIKAGIDP 354 AQ + I ++ + P +++A+M+++ + MVLD +LI PV PI G DP Sbjct: 306 AQ--ELIEGLMNMVPGGPWGIIIAMMVIVFLLAMVLDPVGIMLITLPVFMPIVESLGFDP 363 Query: 355 VYFGVMFVLIGSIGLITPPVGTVLNVVGGI--GRLRMETLVRGVMPFFLIYLVIVGLLIA 412 ++FG++FV+ IG +TPP G L + GI + M+ + + ++PF ++ +V + L++ Sbjct: 364 IWFGILFVINMEIGYMTPPFGFNLFYLKGIVPPSITMKDIYKSIIPFVIVEIVGIILIMV 423 Query: 413 VPSIIT 418 P I T Sbjct: 424 FPEIAT 429 Lambda K H 0.328 0.142 0.413 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: 571 Number of extensions: 44 Number of successful extensions: 6 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: 425 Length of database: 436 Length adjustment: 32 Effective length of query: 393 Effective length of database: 404 Effective search space: 158772 Effective search space used: 158772 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 (21.7 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