Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate Ac3H11_605 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_605 Length = 345 Score = 320 bits (821), Expect = 2e-92 Identities = 171/309 (55%), Positives = 219/309 (70%), Gaps = 4/309 (1%) Query: 6 LPLMITIGVFVLGYLYCLTQFPGFASTRVICNILTDNAFLGIIAVGMTFVILSGGIDLSV 65 LPL TI +FV + GF S +V N+L DNAFL I+AVGMTFVILSGGIDLSV Sbjct: 32 LPLAATISLFVAMATLGSVLYTGFFSAQVFLNLLIDNAFLIIVAVGMTFVILSGGIDLSV 91 Query: 66 GSVIAFTGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLAGMF 125 GSV+A T + LA ++ G +P++A PLVL+MG AFGAFMG LI+ ++ FI+TLAGMF Sbjct: 92 GSVVALTTMVLAALVEHRGWNPMVAIPLVLLMGTAFGAFMGFLIERFRLQPFIVTLAGMF 151 Query: 126 FLRGVSYLVSEESIPINHPIYDTLSSLAWKIP--GGGRLSAMGLLMLAVVVIGIFLAHRT 183 RG+ YL+S +SI I H Y L+ W++P G LS L+ +AV+++ +F+AH T Sbjct: 152 LARGLCYLISIDSISITHEGYSELAQ--WRLPLWEGASLSLGALIAIAVLLVALFVAHCT 209 Query: 184 RFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYALAGVGV 243 FG VYA+GG+ SA LMG+ R T I +Y LS + LAG+VF+ Y +GY L VG+ Sbjct: 210 PFGRSVYAVGGSEHSAVLMGLPVRRTLIGVYTLSGFCSALAGVVFTFYMLSGYGLHAVGM 269 Query: 244 ELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAIGILLFI 303 ELDAIA+VVIGGTLL+GGVG V GTLFGV + G+IQT I+FDGTLSSWWT+I +G+LLF Sbjct: 270 ELDAIAAVVIGGTLLTGGVGYVAGTLFGVLMLGIIQTLISFDGTLSSWWTRIVVGVLLFA 329 Query: 304 FIALQRGLT 312 F LQR L+ Sbjct: 330 FCLLQRLLS 338 Lambda K H 0.329 0.145 0.428 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: 378 Number of extensions: 19 Number of successful extensions: 1 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: 331 Length of database: 345 Length adjustment: 28 Effective length of query: 303 Effective length of database: 317 Effective search space: 96051 Effective search space used: 96051 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