Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate HSERO_RS03645 HSERO_RS03645 ribose ABC transporter permease
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__HerbieS:HSERO_RS03645 Length = 339 Score = 157 bits (398), Expect = 3e-43 Identities = 108/308 (35%), Positives = 163/308 (52%), Gaps = 12/308 (3%) Query: 6 LPLMITIGVFVLGYLYCLTQ--FPGFASTRVICNILTDNAFLGIIAVGMTFVILSGGIDL 63 LP+++ + + G L+ FAS NIL A ++A GMTFVIL+ GIDL Sbjct: 30 LPVLVVLYLLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDL 89 Query: 64 SVGSVIAFTGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLAG 123 SVGSV+A + V +V G +P A P+ + G G G ++ L I AF++TL Sbjct: 90 SVGSVLAVSAVLGMQV--SLGAAPGWAIPMFIFSGLVMGMVNGAMVALLNINAFVVTLGT 147 Query: 124 MFFLRGVSYLVSEESIPINHPIYDTLSSLAWKIPGGGRLSAMGLLMLAVVVIGI--FLAH 181 M RG +YL+++ + +N+ I S W I G L L+ +AV V+ + + Sbjct: 148 MTAFRGAAYLLADGTTVLNNDI----PSFEW-IGNGDFLHVPWLIWVAVAVVLLSWVILR 202 Query: 182 RTRFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYALAGV 241 +T G +YAIGGN +A L GI + +Y +S + LAG + + G Sbjct: 203 KTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGS 262 Query: 242 GVELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAIGILL 301 G ELDAIA+VV+GGT L GGVG++ GT+ G I G++ + G LSS+W +A G ++ Sbjct: 263 GYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILG-LSSFWQYVAKGAVI 321 Query: 302 FIFIALQR 309 + + L + Sbjct: 322 VLAVILDK 329 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: 328 Number of extensions: 27 Number of successful extensions: 5 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: 339 Length adjustment: 28 Effective length of query: 303 Effective length of database: 311 Effective search space: 94233 Effective search space used: 94233 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