Align Inner-membrane translocator (characterized, see rationale)
to candidate GFF2276 PGA1_c23080 ribose transport system permease protein RbsC
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__Phaeo:GFF2276 Length = 324 Score = 129 bits (323), Expect = 1e-34 Identities = 93/303 (30%), Positives = 151/303 (49%), Gaps = 13/303 (4%) Query: 15 LLLTMFLVG-TFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALS 73 + +F++G T F + N++R +A L + ALG+T V+ISG +DLSVG++++ S Sbjct: 20 IAFALFIIGFTIANPKFLTLDNFENVVRSSAILGVMALGVTFVVISGNLDLSVGSMMSFS 79 Query: 74 GVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLARGLAT 133 +V +L + P LA + + GAL+G ++ KL IVTL + GL Sbjct: 80 TIV--VLDLHDKLGPTLAIPAMFAMTLCLGALIGFLVGYLKLNSLIVTLGMLSAIHGLTL 137 Query: 134 TLS---EESIAIDHPFYDAVAEMSIALPGNGALDLSSLIFILFFVIIAVVMHYTRFGTNV 190 T S IA + A+ L + LIFI ++ +++ T FG V Sbjct: 138 TYSGGKNMDIADKEGTWFAIFGQGNIL----GIQTPILIFIALAALLGIILAKTPFGRKV 193 Query: 191 YAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVELDAIA 250 YA+GGN +A GI A+ Y +S+ AG++ + G+EL+ +A Sbjct: 194 YAVGGNGTAATFSGIRRARVVFLCYIMSALCVATAGLIQASRSMGSQNTVGQGLELEVLA 253 Query: 251 AVVIGGTLLTGGSGFVLGTVLGVILMGVIQT---YITFDGSLSSWWTKIVIGLLLFFFIL 307 AV++GG L GGSG + TV+GV+++G IQ + D S+ T I+I L ++ I Sbjct: 254 AVILGGASLLGGSGTIFKTVIGVLILGFIQNGLLLVGLDFSVQYVVTWIIIILAVWLDIA 313 Query: 308 LQK 310 ++ Sbjct: 314 AKR 316 Lambda K H 0.330 0.145 0.424 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: 322 Number of extensions: 29 Number of successful extensions: 4 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: 320 Length of database: 324 Length adjustment: 28 Effective length of query: 292 Effective length of database: 296 Effective search space: 86432 Effective search space used: 86432 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: 48 (23.1 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