Align major cell-binding factor (characterized)
to candidate PP_0227 PP_0227 periplasmic cystine-binding protein
Query= CharProtDB::CH_021449 (259 letters) >FitnessBrowser__Putida:PP_0227 Length = 264 Score = 91.7 bits (226), Expect = 1e-23 Identities = 77/253 (30%), Positives = 124/253 (49%), Gaps = 19/253 (7%) Query: 3 FRKSLLKLAVFALGACVAFSNANAAEGKLESIKSKGQLIVGVKNDVPHYALLDQATGEIK 62 F K LL ++ L S A A E +L++I+ KG + VG++ P ++ D+ G++ Sbjct: 4 FAKPLLNASLALLLGAGLLSQAFAGE-QLKTIQEKGVINVGLEGTYPPFSFQDE-NGKLT 61 Query: 63 GFEVDVAKLLAKSILGDDKKIKLVAVNAKTRGPL--LDNGSVDAVIATFTITPERKRIYN 120 GFEV++++LLAK LG KI+ K G L L++ +D V+ TI+ ERK+ Y+ Sbjct: 62 GFEVELSELLAKE-LGVKAKIQ----PTKWDGILAALESKRLDVVVNQVTISEERKKKYD 116 Query: 121 FSEPYYQDAIGLLVLKEK----KYKSLADMKGANIGVAQAATTKKAIGEAAKKIGIDVKF 176 FSEPY I L+LK+K K D+ G +GV ++ + KK Sbjct: 117 FSEPYTVSGIQALILKKKAEQLNIKGAQDLAGKKVGVGLGTNYEQWV----KKDVPQADV 172 Query: 177 SEFPDYPSIKAALDAKRVDAFSVDKSILLGYVD--DKSEILPDSFEPQSYGIVTKKDDPA 234 + D PS A L R+DA +D+ L Y +E+ D+F G+ +K +P Sbjct: 173 RTYEDDPSKFADLRNGRIDAILIDRLAALEYAQKAKDTELAGDAFSRLESGVALRKGEPE 232 Query: 235 FAKYVDDFVKEHK 247 ++ + + K Sbjct: 233 LLAAINKAIDKLK 245 Lambda K H 0.316 0.135 0.372 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: 169 Number of extensions: 10 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: 259 Length of database: 264 Length adjustment: 25 Effective length of query: 234 Effective length of database: 239 Effective search space: 55926 Effective search space used: 55926 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 47 (22.7 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