Align D-mannose and D-mannitol transporter (characterized)
to candidate PP_2837 PP_2837 putative uronate transporter
Query= reanno::pseudo5_N2C3_1:AO356_28540 (430 letters) >FitnessBrowser__Putida:PP_2837 Length = 436 Score = 205 bits (521), Expect = 3e-57 Identities = 122/403 (30%), Positives = 199/403 (49%), Gaps = 14/403 (3%) Query: 8 LIIIMLFLAGVINYLDRSALSVAAPFIQKDYGLSTGEMGMIFSSFFVGYAAFNFIGGWAA 67 + ++ L L G++NYLDRSALS+A IQKD +S +MG++ S+F + YA G Sbjct: 10 ITVVFLLLIGIVNYLDRSALSIANTSIQKDMMISPSQMGILLSAFSIAYAFAQLPMGMII 69 Query: 68 DRYGAKTTLLLAMVLWSLFSGLTVLTVGFASLVLIRILFGMGEGPLSVTTSKMVNNWYTP 127 DR G+K L +++ WS+ + FA + +R+L G+GE P+ + +K ++ W+ Sbjct: 70 DRLGSKIALGASLLGWSVAQAAFGMVNSFAGFMGLRVLLGIGEAPMFPSAAKALSEWFDA 129 Query: 128 KRRARAIGASMSGTPLGGAISGPVVGFIAVTYGWKISFIIIMLIGLVWAAVWFKFVKERP 187 R G S T LG ++ P++ V +GW+ FII +IG+V A W F K + Sbjct: 130 NERGTPTGVVWSSTCLGPCLAPPLLTLFMVNFGWRGMFIITGVIGVVLALCWLTFYKSKA 189 Query: 188 EGEGAEDILRAEGQ----GELAAQPVFPLRFY-------LKQPTVLFTSLAFFSYNYTLF 236 L AEG+ AA P Y K + L F Y L+ Sbjct: 190 RFLAE---LAAEGKPLPSERQAAAATAPKASYFAGWLDLFKHRSTWGAVLGFMGVIYMLW 246 Query: 237 FFLTWFPSYLTMAHGLNVKDMSIATVIPWVLGFLGLALGGFISDFVFKKTGRMMFSRKVV 296 LTW P Y HGL++ + + + G G + G D++ ++ ++ SRK Sbjct: 247 LHLTWLPGYFEREHGLDLYKTAWVVSLAYGFGAAGTIVAGRFCDWLVRRGMSVLGSRKFS 306 Query: 297 LVTCLLACAVCIACAGMVTTLYPAVILVALAVFFLYLTGAIYWAIIQDTVPAARVGGVSG 356 ++T L+ A+ VT L ++L+ LA+F + + A W I+ V + RV Sbjct: 307 VITGLVLAALFTLPLSFVTGLTGCIMLLCLALFSINMASATAWMIVNTIVDSQRVASFGS 366 Query: 357 FMHFLANTSGIVGPTLTGFLVQFTGSFTSAFLLAGLLTVIGAV 399 +F +G V P +TGF +Q++GSFT+AF+++ ++ + AV Sbjct: 367 IQNFGGYIAGSVAPIVTGFSIQYSGSFTTAFMISAVVALCSAV 409 Score = 28.5 bits (62), Expect = 4e-04 Identities = 33/158 (20%), Positives = 64/158 (40%), Gaps = 10/158 (6%) Query: 33 FIQKDYGLSTGEMGMIFSSFFVGYAAFNFIGGWAAD---RYGA------KTTLLLAMVLW 83 + ++++GL + + S + AA + G D R G K +++ +VL Sbjct: 255 YFEREHGLDLYKTAWVVSLAYGFGAAGTIVAGRFCDWLVRRGMSVLGSRKFSVITGLVLA 314 Query: 84 SLFSGLTVLTVGFASLVLIRILFGMGEGPLSVTTSKMVNNWYTPKRRARAIGASMSGTPL 143 +LF+ G +++ L S T +VN +R A G + Sbjct: 315 ALFTLPLSFVTGLTGCIMLLCLALFSINMASATAWMIVNTIVDSQRVASFGSIQNFGGYI 374 Query: 144 GGAISGPVVGF-IAVTYGWKISFIIIMLIGLVWAAVWF 180 G+++ V GF I + + +F+I ++ L A +F Sbjct: 375 AGSVAPIVTGFSIQYSGSFTTAFMISAVVALCSAVAYF 412 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: 532 Number of extensions: 25 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 430 Length of database: 436 Length adjustment: 32 Effective length of query: 398 Effective length of database: 404 Effective search space: 160792 Effective search space used: 160792 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