Align Inner-membrane translocator (characterized, see rationale)
to candidate Pf1N1B4_6033 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6033 Length = 325 Score = 124 bits (311), Expect = 3e-33 Identities = 91/306 (29%), Positives = 151/306 (49%), Gaps = 6/306 (1%) Query: 13 ASLLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIAL 72 A LL M + + F S + L L++ A+GMT V+I GGIDLSVG+V+AL Sbjct: 24 AGALLAMVALFSVLSSHFLSYDTFSTLANQIPDLMVLAVGMTFVLIIGGIDLSVGSVLAL 83 Query: 73 SGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLARGLA 132 + S+ I + W L A ++ + + L G + G+I +++ FIV+L + +ARGLA Sbjct: 84 AASAVSVAILGWGWSVLPAALLGMAVAALAGTITGSITVAWRIPSFIVSLGVLEMARGLA 143 Query: 133 TTLSEESIAIDHPFYDAVAEMSIALPGNGALDLSSLIFILFFVIIAVVMHYTRFGTNVYA 192 ++ A Y A ++ P + S +I +L I V+ T FG + Sbjct: 144 YQMTGSRTA-----YIGDAFAWLSNPIAFGISPSFIIALLIIFIAQAVLTRTVFGRYLIG 198 Query: 193 IGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVELDAIAAV 252 IG N+ + L GI+ I ++++ LA +A + + G+EL IAAV Sbjct: 199 IGTNEEAVRLAGINPKPYKILVFSLMGLLAGIAALFQISRLEAADPNAGSGLELQVIAAV 258 Query: 253 VIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFFFILLQKLL 312 VIGGT L GG G V+ T GV+++ V+ + G+ +I+ G ++ ++L Sbjct: 259 VIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEP-TKRIITGAVIVVAVVLDTYR 317 Query: 313 NGRKTQ 318 + R ++ Sbjct: 318 SQRASR 323 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: 321 Number of extensions: 16 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: 320 Length of database: 325 Length adjustment: 28 Effective length of query: 292 Effective length of database: 297 Effective search space: 86724 Effective search space used: 86724 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