Align D-mannose and D-mannitol transporter (characterized)
to candidate PP_3600 PP_3600 glucarate transporter
Query= reanno::pseudo5_N2C3_1:AO356_28540 (430 letters) >FitnessBrowser__Putida:PP_3600 Length = 454 Score = 201 bits (512), Expect = 3e-56 Identities = 131/436 (30%), Positives = 207/436 (47%), Gaps = 24/436 (5%) Query: 6 RSLIIIMLFLAGVINYLDRSALSVAAPFIQKDYGLSTGEMGMIFSSFFVGYAAFNFIGGW 65 R LI+ MLFL INY DR+ +++A +QKD G+ +G IFS+F Y A GGW Sbjct: 10 RYLILFMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQIPGGW 69 Query: 66 AADRYGAKTTLLLAMVLWSLFSGLTVLTVGF------ASLVLIRILFGMGEGPLSVTTSK 119 DR+G+K ++ WSLF+ L G +L +R L G E P ++ Sbjct: 70 LLDRFGSKNVYAFSIFTWSLFTLLQGFVGGLPVAWAVVTLFTLRFLVGFAEAPSFPGNAR 129 Query: 120 MVNNWYTPKRRARAIGASMSGTPLGGAISGPVVGFIAVTYGWKISFIIIMLIGLVWAAVW 179 +V W+ + R A S A+ P++G+I ++GW+ F+++ ++G++++ VW Sbjct: 130 IVAAWFPTQERGTASAIFNSAQYFATALFAPIMGWIVFSFGWEHVFVVMGVLGIIFSMVW 189 Query: 180 FKFV---KERPEGEGAEDILRAEGQGELAAQPV-----FPLRFYLKQ----PTVLFTSLA 227 K + ++ P +E + E G L P Y+KQ +L L Sbjct: 190 LKTIYNPRQHPRISQSE-LEHIEQNGGLVDMDQKRGSDGPKWGYIKQLLTSRMLLGVYLG 248 Query: 228 FFSYNYTLFFFLTWFPSYLTMAHGLNVKDMSIATVIPWVLGFLGLALGGFISDFVFKKTG 287 + N +FFLTWFP YL G+ + +P V GF+G LGG ISD++ ++ Sbjct: 249 QYCINAITYFFLTWFPVYLVQERGMTILKAGFIASLPAVCGFIGGVLGGVISDWLLRRGN 308 Query: 288 RMMFSRKVVLVTCLLACAVCIACAGMVTTLYPAVILVALAVFFLYLTGAIYWAIIQDTVP 347 + FSRK+ +V LL + C V + V + LA FF GA+ WA++ DT P Sbjct: 309 SLTFSRKLPIVCGLLLSTTMVFC-NYVDAEWMVVGFMTLA-FFGKGIGALGWAVVADTSP 366 Query: 348 AARVGGVSGFMHFLANTSGIVGPTLTGFLVQFTGSFTSAFLLAGLLTVIGAVCVARYVKP 407 G G + N + I P + G+++ TGSF A + G ++ V P Sbjct: 367 KQIAGLSGGLFNTFGNIASITTPIVIGYIISATGSFKWALVYVGANALVAVFSYLVIVGP 426 Query: 408 LSVADTGNAAAQSPQP 423 + + +AA P+P Sbjct: 427 IKRIELRDAA---PKP 439 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: 594 Number of extensions: 34 Number of successful extensions: 5 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: 430 Length of database: 454 Length adjustment: 32 Effective length of query: 398 Effective length of database: 422 Effective search space: 167956 Effective search space used: 167956 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