Align RhaQ (characterized, see rationale)
to candidate GFF2276 PGA1_c23080 ribose transport system permease protein RbsC
Query= uniprot:Q7BSH2 (337 letters) >FitnessBrowser__Phaeo:GFF2276 Length = 324 Score = 145 bits (365), Expect = 2e-39 Identities = 103/310 (33%), Positives = 165/310 (53%), Gaps = 11/310 (3%) Query: 31 LLFAVAVLIFVFNSLASPYFLDAWNLSDATFNFTEKAMIAFAMALLVISGEIDLSVAAII 90 +L A A+ I F ++A+P FL N + + ++A + +VISG +DLSV +++ Sbjct: 18 ILIAFALFIIGF-TIANPKFLTLDNFENVVRSSAILGVMALGVTFVVISGNLDLSVGSMM 76 Query: 91 ALASTAMGAAVQIGIGTPGLVLIGIGTGLACGVFNGVLVSVLKLPSIVVTIGTMSLFRGI 150 + ST + + +G + L G G LV LKL S++VT+G +S G+ Sbjct: 77 SF-STIVVLDLHDKLGPTLAIPAMFAMTLCLGALIGFLVGYLKLNSLIVTLGMLSAIHGL 135 Query: 151 SYIVLGDQAYG---KYPADFAYFGQGYVVWVFSFEFVLFIVLAVLFAILLHATNFGRQVY 207 + G + K FA FGQG ++ + + ++FI LA L I+L T FGR+VY Sbjct: 136 TLTYSGGKNMDIADKEGTWFAIFGQGNILGIQT-PILIFIALAALLGIILAKTPFGRKVY 194 Query: 208 AIGNNDFAARFSGIPVERVKSILFLLTGIMSGIAAVCLTSRLGSTRPSIAQGWELEVVTM 267 A+G N AA FSGI RV + ++++ + A + SR ++ ++ QG ELEV+ Sbjct: 195 AVGGNGTAATFSGIRRARVVFLCYIMSALCVATAGLIQASRSMGSQNTVGQGLELEVLAA 254 Query: 268 VVLGGISILGGFRHDRGVF--VIAAFVMGLVTFGLGLLNLPGIVMSIFIGLLIIVTIAIP 325 V+LGG S+LGG +F VI ++G + GL L+ L V + ++II+ + + Sbjct: 255 VILGGASLLGG---SGTIFKTVIGVLILGFIQNGLLLVGLDFSVQYVVTWIIIILAVWLD 311 Query: 326 IIARRIKLMS 335 I A+R KLMS Sbjct: 312 IAAKRGKLMS 321 Lambda K H 0.330 0.145 0.423 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: 288 Number of extensions: 21 Number of successful extensions: 3 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: 337 Length of database: 324 Length adjustment: 28 Effective length of query: 309 Effective length of database: 296 Effective search space: 91464 Effective search space used: 91464 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: 49 (23.5 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