Align D-mannose and D-mannitol transporter (characterized)
to candidate HSERO_RS02860 HSERO_RS02860 MFS transporter
Query= reanno::pseudo5_N2C3_1:AO356_28540 (430 letters) >FitnessBrowser__HerbieS:HSERO_RS02860 Length = 398 Score = 195 bits (496), Expect = 2e-54 Identities = 120/383 (31%), Positives = 199/383 (51%), Gaps = 17/383 (4%) Query: 6 RSLIIIMLFLAGVINYLDRSALSVAAPFIQKDYGLSTGEMGMIFSSFFVGYAAFNFIGGW 65 + + + LFLA + Y DR +S A I K++ L + GM+ S+F+V YA +GGW Sbjct: 10 KMICLSALFLAWAVGYADRIVMSTAIIPISKEFALDAQQAGMVLSAFYVSYALMQLMGGW 69 Query: 66 AADRYGAKTTLLLAMVLWSLFSGLTVLTVGFASLVLIRILFGMGEGPLSVTTSKMVNNWY 125 +DRYG++ +++ +V WSLF+GLT + FASL+LIR LFG GEG S +S V + Sbjct: 70 LSDRYGSRIVVVMCVVAWSLFTGLTSMAWSFASLLLIRFLFGAGEGCFSPASSVTVAEVF 129 Query: 126 TPKRRARAIGASMSGTPLGGAISGPVVGFIAVTYGWKISFIIIMLIGLVWAAVWFKFVKE 185 + RARA +S LG A+ +V V GW+ +F I+ +G++ AA+ + ++ Sbjct: 130 PQQERARAKSFLISTVFLGNAVGSGMVALTVVYLGWRGTFHILAFVGMIVAAILWLALR- 188 Query: 186 RPEGEGAEDILRAEGQGELAAQPVFPLRFYLKQPTVLFTSLAFFSYNYTLFFFLTWFPSY 245 G A+ Q AA+P LR +K PT L + +F + ++W PS+ Sbjct: 189 --SGMAAQ-------QARSAARPKNQLRELVKNPTALRLTAIWFCTSIVYIGMISWMPSF 239 Query: 246 LTMAHGLNVKDMSIATVIPWVLGFLGLALGGFISDFVFKKTGRMMFSRKVVLVTCLLACA 305 L + +++ + IA+ IP++L FLG + G++ D K G+ K ++ LACA Sbjct: 240 LLKVYQIDLLHIGIASAIPYLLAFLGTNVVGWLLD----KHGK--GREKYFMMGGALACA 293 Query: 306 VCIACAGMVTTLYPAVILVALAVFFLYLTGAIYWAIIQDTVPAARVGGVSGFMHFLANTS 365 V +A T + V+ L + A +++ P+ +G +G M+F + Sbjct: 294 VFLALMISTTVIELLVVYWTLCLLSFNFVYATVFSVPLKHFPSHLIGSATGLMNFGGQLA 353 Query: 366 GIVGPTLTG-FLVQFTGSFTSAF 387 G + P + G +V F G++ +AF Sbjct: 354 GSIAPVVMGSLIVAFNGAYLAAF 376 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: 511 Number of extensions: 27 Number of successful extensions: 2 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: 398 Length adjustment: 31 Effective length of query: 399 Effective length of database: 367 Effective search space: 146433 Effective search space used: 146433 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: 50 (23.9 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