Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate PP_2761 PP_2761 putative Ribose ABC transporter, permease protein
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__Putida:PP_2761 Length = 328 Score = 113 bits (282), Expect = 7e-30 Identities = 98/305 (32%), Positives = 152/305 (49%), Gaps = 18/305 (5%) Query: 4 RNLPLMITIGVFVLGYLYCLTQFPGFASTRVICNILTDN-AFLGIIAVGMTFVILSGGID 62 R L ++ +F L+ + PGF + + ++L +N L I+A+GMT+ I +GGID Sbjct: 19 RALLRLVMPTLFAAVLLFFALKAPGFLTVGNLSSLLLNNFVLLAIVAIGMTYAIAAGGID 78 Query: 63 LSVGSVIAFTGV-FLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITL 121 LSVG+ + F+ + F+ + FGL +A P L+ G G F LI L+I F+ TL Sbjct: 79 LSVGTALDFSALTFVLLLNAGFGL--YVAIPGGLLAGSLAGLFNAGLIAGLRISPFLATL 136 Query: 122 AGMFFLRGVSYLVSEESIPINHPIYDTLSSLAWKIPGGGRLSAMGLLMLAVVVIGIFLAH 181 +F V L+SE PI + S LA + G L + L+ L +V G+ LA Sbjct: 137 GTLFIGSSVQKLLSEGGQPI-YLEAQVRSGLATERMLGVPLPLL-LVALLALVYGVVLA- 193 Query: 182 RTRFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYALAGV 241 R R G ++ +G A G++ R +++ S + LAGI+ A ++G Sbjct: 194 RGRLGREIIVLGSQPLVARYSGLAQRRIAALVFIASAFASALAGILLPATVNAYAPMSGN 253 Query: 242 GVELDAIASVVIGGTL-LSGGV---GTVLGTLF-GVAIQGLIQTYINFDGTLSSWWTKIA 296 ++AI +V IG TL L V GT+LG LF V GL+ NF +W ++A Sbjct: 254 AFLMNAIGAVFIGATLSLHNRVNVPGTLLGVLFLNVTANGLLLIGWNF------FWQQVA 307 Query: 297 IGILL 301 G+L+ Sbjct: 308 TGVLI 312 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: 312 Number of extensions: 26 Number of successful extensions: 4 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