Align D-mannose and D-mannitol transporter (characterized)
to candidate HSERO_RS15805 HSERO_RS15805 glucarate transporter
Query= reanno::pseudo5_N2C3_1:AO356_28540 (430 letters) >FitnessBrowser__HerbieS:HSERO_RS15805 Length = 447 Score = 207 bits (526), Expect = 7e-58 Identities = 133/430 (30%), Positives = 213/430 (49%), Gaps = 26/430 (6%) Query: 6 RSLIIIMLFLAGVINYLDRSALSVAAPFIQKDYGLSTGEMGMIFSSFFVGYAAFNFIGGW 65 R LI+ +LF+ +NY DR+ LS+A ++ + L MG IFS+F Y GGW Sbjct: 20 RYLILFLLFVVTTVNYADRATLSIAGSAMKTELSLDPVMMGYIFSAFSWAYVLAQLPGGW 79 Query: 66 AADRYGAKTTLLLAMVLWSLF----SGLTVLT--VGFASLVLIRILFGMGEGPLSVTTSK 119 DR+G+K + ++ LWS+F +G+T ++ ASL L+R + G+ E P + Sbjct: 80 LLDRFGSKKIYMWSIALWSVFTFLQAGVTWMSTAAAVASLFLLRFMVGLAEAPSFPANGR 139 Query: 120 MVNNWYTPKRRARAIGASMSGTPLGGAISGPVVGFIAVTYGWKISFIIIMLIGLVWAAVW 179 +V W+ K R A S + P++ +I TY W F ++ ++G+ A +W Sbjct: 140 IVAAWFPTKERGTASAIFNSAQYFAAVLFTPLMAWIVHTYSWHHVFTVMGVVGIALALIW 199 Query: 180 FKFV---KERPEGEGAEDILRAEGQGEL-------AAQPVFPLRFYLKQ----PTVLFTS 225 + + K+ P AE + E G L A P R Y++Q +L Sbjct: 200 GRIIYSPKDHPRINQAE-LAHIESGGGLVDMDNRKVAAPSTKGRGYIRQLLSNRMLLGVY 258 Query: 226 LAFFSYNYTLFFFLTWFPSYLTMAHGLNVKDMSIATVIPWVLGFLGLALGGFISDFVFKK 285 + + N +FFLTWFP YL G+++ IP V GF+G +GG ISD + K+ Sbjct: 259 IGQYCINVITYFFLTWFPVYLVQERGMSILKAGFVASIPAVCGFIGGVVGGLISDRLIKR 318 Query: 286 TGRMMFSRKVVLVTCLLACAVCIACAGMVTTLYPAVILVALAVFFLYLTGAIYWAIIQDT 345 + ++RK+ +V +L I C V + V ++ALA FF GA+ WA++ DT Sbjct: 319 GLSVTWARKIPIVGGMLLSMTMILC-NYVEAQWMVVGIMALA-FFGKGVGALGWAVVADT 376 Query: 346 VPAARVGGVSGFMHFLANTSGIVGPTLTGFLVQFTGSFTSAFLLAG---LLTVIGAVCVA 402 P VG G + N +GI P + G++V+ TGSF+ A + G L+TVI + + Sbjct: 377 APKQIVGLSGGLFNMFGNVAGITTPIVIGYIVKETGSFSGALVFVGINALVTVISYLVIV 436 Query: 403 RYVKPLSVAD 412 + +K + + D Sbjct: 437 KEIKRVELKD 446 Lambda K H 0.329 0.142 0.439 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: 599 Number of extensions: 36 Number of successful extensions: 4 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: 430 Length of database: 447 Length adjustment: 32 Effective length of query: 398 Effective length of database: 415 Effective search space: 165170 Effective search space used: 165170 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