Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate PfGW456L13_3910 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3910 Length = 325 Score = 118 bits (296), Expect = 2e-31 Identities = 84/251 (33%), Positives = 131/251 (52%), Gaps = 8/251 (3%) Query: 24 TQFPGFASTRVICNILTDNAFLGIIAVGMTFVILSGGIDLSVGSVIAFTGVFLAKVIGDF 83 + F + + + N + D L ++AVGMTFV++ GGIDLSVGSV+A ++ I + Sbjct: 39 SHFLSYDTFSTLANQIPD---LMVLAVGMTFVLIIGGIDLSVGSVLALAASTVSVAILGW 95 Query: 84 GLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLAGMFFLRGVSYLVSEESIPINH 143 G L A L + + G G + A +IP+FI++L + RGV+Y ++ Sbjct: 96 GWGVLPAALLGMAVAALAGTITGSITVAWRIPSFIVSLGVLEMARGVAYQMTGSRTAY-- 153 Query: 144 PIYDTLSSLAWKIPGGGRLSAMGLLMLAVVVIGIFLAHRTRFGNQVYAIGGNATSANLMG 203 I D + L+ I G +S ++ L ++ + + RT FG + IG N + L G Sbjct: 154 -IGDAFAWLSNPIAFG--ISPSFIIALLIIFVAQAVLTRTVFGRYLIGIGTNEEAVRLAG 210 Query: 204 ISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYALAGVGVELDAIASVVIGGTLLSGGVG 263 I+ + + ++ L LA +A + +A AG G+EL IA+VVIGGT L GG G Sbjct: 211 INPKPYKVLVFSLMGLLAGVAALFQISRLEAADPNAGSGLELQVIAAVVIGGTSLMGGRG 270 Query: 264 TVLGTLFGVAI 274 +V+ T FGV I Sbjct: 271 SVISTFFGVLI 281 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: 281 Number of extensions: 17 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: 325 Length adjustment: 28 Effective length of query: 303 Effective length of database: 297 Effective search space: 89991 Effective search space used: 89991 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