Align Inner-membrane translocator (characterized, see rationale)
to candidate Ac3H11_605 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_605 Length = 345 Score = 338 bits (868), Expect = 8e-98 Identities = 168/314 (53%), Positives = 232/314 (73%) Query: 5 RFIPLWITASLLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDL 64 +++PL T SL + M +G+ + GF S +V NLL DNAFL+I A+GMT VI+SGGIDL Sbjct: 30 KYLPLAATISLFVAMATLGSVLYTGFFSAQVFLNLLIDNAFLIIVAVGMTFVILSGGIDL 89 Query: 65 SVGAVIALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAG 124 SVG+V+AL+ +V + L+ W+P++A ++L +GT FGA MG +I ++LQPFIVTLAG Sbjct: 90 SVGSVVALTTMVLAALVEHRGWNPMVAIPLVLLMGTAFGAFMGFLIERFRLQPFIVTLAG 149 Query: 125 MFLARGLATTLSEESIAIDHPFYDAVAEMSIALPGNGALDLSSLIFILFFVIIAVVMHYT 184 MFLARGL +S +SI+I H Y +A+ + L +L L +LI I ++ V H T Sbjct: 150 MFLARGLCYLISIDSISITHEGYSELAQWRLPLWEGASLSLGALIAIAVLLVALFVAHCT 209 Query: 185 RFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGV 244 FG +VYA+GG++HSA LMG+ + +T I +Y +S F + LAG+VFTFY SGY L A+G+ Sbjct: 210 PFGRSVYAVGGSEHSAVLMGLPVRRTLIGVYTLSGFCSALAGVVFTFYMLSGYGLHAVGM 269 Query: 245 ELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFF 304 ELDAIAAVVIGGTLLTGG G+V GT+ GV+++G+IQT I+FDG+LSSWWT+IV+G+LLF Sbjct: 270 ELDAIAAVVIGGTLLTGGVGYVAGTLFGVLMLGIIQTLISFDGTLSSWWTRIVVGVLLFA 329 Query: 305 FILLQKLLNGRKTQ 318 F LLQ+LL+ R ++ Sbjct: 330 FCLLQRLLSRRSSK 343 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: 440 Number of extensions: 20 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: 320 Length of database: 345 Length adjustment: 28 Effective length of query: 292 Effective length of database: 317 Effective search space: 92564 Effective search space used: 92564 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