Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__Phaeo:GFF2274 Length = 503 Score = 300 bits (768), Expect = 8e-86 Identities = 177/502 (35%), Positives = 285/502 (56%), Gaps = 9/502 (1%) Query: 8 LTSSVPVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPD 67 +T PV+ + K F AL+ VS+ ++PGE HAL+G NGAGKSTL+ +L G+ +PD Sbjct: 1 MTEQSPVLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPD 60 Query: 68 TGEVRFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPL-RGGVIDWQA 126 G++ + DA + + ++Q ++ +LSVAEN+++ P R G++DW Sbjct: 61 EGQIIVAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAE 120 Query: 127 MRRDARALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEI 186 + A+L+ K+ R GDLS+ +Q+VEIARAL+ A+ +I DEPTA L E Sbjct: 121 LEAKTNAILEKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEK 180 Query: 187 KRLFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAM 246 LF IS+LQ +GV +ISH ++E+++I ++VLRD ++ + + E + + M Sbjct: 181 VVLFEVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMM 240 Query: 247 TGERGGLAVADAAARGALPADTAVALELKELT-GADYEGVSFTVKRGEVVGLTGATSSGR 305 G + D + A VALE++ L+ G+ +E V+F V+RGEVVG G +GR Sbjct: 241 IGRK-----LDLSRNEAHHELGEVALEVRGLSCGSLFEDVNFEVRRGEVVGFYGLVGAGR 295 Query: 306 TSVAEAIAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENA 365 T +AE + GLR G+I +DGA + ++ GI VP+DR +GLVL + +N Sbjct: 296 TEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRDNM 355 Query: 366 SMTIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALAT 425 ++ L A + A + D L I G + +V LSGGNQQK+V+ + L+ Sbjct: 356 TLPQVDDLKAGPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSM 415 Query: 426 NPNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGR 484 PNVL++ +PT G+DV SK + +++ + +G AV+V+S E+ + L DR++ M+ GR Sbjct: 416 RPNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGR 475 Query: 485 VAAEFPA-GWQDHDLIASVEGV 505 + F + + +LIA++ G+ Sbjct: 476 IMRTFTSEEVTEENLIAAISGL 497 Lambda K H 0.318 0.134 0.377 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: 575 Number of extensions: 28 Number of successful extensions: 8 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: 510 Length of database: 503 Length adjustment: 34 Effective length of query: 476 Effective length of database: 469 Effective search space: 223244 Effective search space used: 223244 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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