Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate HSERO_RS05325 HSERO_RS05325 ribose ABC transporter permease
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__HerbieS:HSERO_RS05325 Length = 328 Score = 166 bits (420), Expect = 7e-46 Identities = 108/280 (38%), Positives = 157/280 (56%), Gaps = 19/280 (6%) Query: 37 NILTDNAFLGIIAVGMTFVILSGGIDLSVGSVIAFTGVFLAKVIGDFGLSPLLAFPLVLV 96 N+L + +GI+AVGM+FVIL+GGIDLSVG+ +A G A +I + GL PL L+ Sbjct: 58 NVLRQVSIVGILAVGMSFVILTGGIDLSVGAAMALAGTISAGLIVNSGLPA----PLALL 113 Query: 97 MGCAFGAFMGLLIDAL----KIPAFIITLAGMFFLRGVSYLVSEESIPINHPIYDTLSSL 152 G +GLL AL ++PA I+TLA M RGV + S +PI + Sbjct: 114 CGVGLATCIGLLNGALVAWGRMPAIIVTLATMGVARGVGLIYSG-----GYPISGLPGWI 168 Query: 153 AWKIPGGGRLSAMG---LLMLAVVVIGIFLAHRTRFGNQVYAIGGNATSANLMGISTRST 209 +W G GR+ + +LML V + L RT FG VYAIGGN +A L G+ T Sbjct: 169 SWF--GVGRIGMVPVPVILMLIVYALAWLLLQRTAFGRHVYAIGGNEMAARLSGVKTTRI 226 Query: 210 TIRIYMLSTGLATLAGIVFSIYTQAGYALAGVGVELDAIASVVIGGTLLSGGVGTVLGTL 269 + +Y +S + LA I+ + +G AGVG ELDAIA+VV+GGT ++GG G V+GTL Sbjct: 227 KLAVYAISGFTSGLAAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIAGGRGLVVGTL 286 Query: 270 FGVAIQGLIQTYINFDGTLSSWWTKIAIGILLFIFIALQR 309 G + G++ +N G ++ + I G+++ + I + R Sbjct: 287 IGAVLLGILNNGLNLMG-INPYLQDIIRGVIILLAIYIAR 325 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: 365 Number of extensions: 27 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: 331 Length of database: 328 Length adjustment: 28 Effective length of query: 303 Effective length of database: 300 Effective search space: 90900 Effective search space used: 90900 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