Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate PP_2456 PP_2456 D-ribose ABC transporter - permease subunit
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__Putida:PP_2456 Length = 331 Score = 121 bits (304), Expect = 2e-32 Identities = 90/289 (31%), Positives = 144/289 (49%), Gaps = 9/289 (3%) Query: 19 YLYCLTQFPGFASTRVICNILTDNAFLGIIAVGMTFVILSGGIDLSVGSVIAFTGVFLAK 78 + + + F + + + N + D L ++AVGMTFV++ GGIDLSVGSV+A ++ Sbjct: 40 FSFLSSHFWSYGTFSTLANQIPD---LMVLAVGMTFVLIIGGIDLSVGSVLALAASTVSV 96 Query: 79 VIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLAGMFFLRGVSYLVSEES 138 I +G L + L + + G+ G + A +IP+FI++L + RG++Y ++ Sbjct: 97 AILGWGWGVLPSALLGMAVAALAGSITGGVTVAWRIPSFIVSLGVLEMARGLAYQFTDSR 156 Query: 139 IPINHPIYDTLSSLAWKIPGGGRLSAMGLLMLAVVVIGIFLAHRTRFGNQVYAIGGNATS 198 Y S+ P +S ++ L V+V+ + RT FG + IG N + Sbjct: 157 TAYIGDAYAWFSN-----PVAFGVSPAFIIALLVIVLAQLVLTRTVFGRYLIGIGTNEEA 211 Query: 199 ANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYALAGVGVELDAIASVVIGGTLL 258 L GI R + ++ L LA LA + +A AG G+EL IA+VVIGGT L Sbjct: 212 VRLAGIDPRPYKVLVFALMGLLAGLAALFQISRLEAADPNAGSGLELQVIAAVVIGGTSL 271 Query: 259 SGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAIGILLFIFIAL 307 GG G+V+ T FGV I ++ + G S +I G ++ I + L Sbjct: 272 MGGRGSVISTFFGVLIISVLAAGLAQIGA-SEPTKRIITGAVIVIAVVL 319 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: 304 Number of extensions: 18 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: 331 Length adjustment: 28 Effective length of query: 303 Effective length of database: 303 Effective search space: 91809 Effective search space used: 91809 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