Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate RR42_RS32890 RR42_RS32890 ABC transporter permease
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__Cup4G11:RR42_RS32890 Length = 322 Score = 145 bits (366), Expect = 1e-39 Identities = 101/298 (33%), Positives = 156/298 (52%), Gaps = 12/298 (4%) Query: 14 VFVLGYLYCLTQFPG--FASTRVICNILTDNAFLGIIAVGMTFVILSGGIDLSVGSVIAF 71 +F LG L L F + I N+L + L ++A G+T VIL+GG+DLSVG+ +A Sbjct: 21 LFALGLLCLLLAVASDAFLTLGNILNVLRQASLLFLLASGVTLVILTGGLDLSVGANVAM 80 Query: 72 TGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLAGMFFLRGVS 131 + A V+ G S +L L G G GLL+ L+IP FI T ++ L GV+ Sbjct: 81 SACVAATVMKATG-STMLGVGAGLGTGALIGLANGLLVAMLRIPPFIATYGMLWVLHGVT 139 Query: 132 Y-LVSEESIPINHPIYDTLSS-LAWKIPGGGRLSAMGLLMLAVVVIGIFLAHRTRFGNQV 189 Y ++ E+I P + + S W +P LML +V G ++ +T +G ++ Sbjct: 140 YWFMAGETIHGFPPAFRAIGSGYLWGVP------IPVYLMLVFLVAGTAMSQKTTYGQEI 193 Query: 190 YAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYALAGVGVELDAIA 249 YAIG N +A L G+ R + +Y++S +A +A +VF + G + L AIA Sbjct: 194 YAIGANPVAARLSGVPVRRRLVLVYLVSGAMAGIASLVFLARLNSAEGDIGEALTLPAIA 253 Query: 250 SVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAIGILLFIFIAL 307 +V+IGGT L GGVG V GTL G I L+ +N T+S+ W + G+++ + + L Sbjct: 254 AVLIGGTSLFGGVGRVSGTLVGAIILTLVLNGMNL-LTVSANWQPLVTGVIVVLAVFL 310 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: 280 Number of extensions: 23 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: 331 Length of database: 322 Length adjustment: 28 Effective length of query: 303 Effective length of database: 294 Effective search space: 89082 Effective search space used: 89082 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