Align major cell-binding factor (characterized)
to candidate YP_004143481.1 Mesci_4321 family 3 extracellular solute-binding protein
Query= CharProtDB::CH_021449 (259 letters) >NCBI__GCF_000185905.1:YP_004143481.1 Length = 260 Score = 93.6 bits (231), Expect = 4e-24 Identities = 78/258 (30%), Positives = 124/258 (48%), Gaps = 21/258 (8%) Query: 10 LAVFALGACVAFSNANAAEGKLESIKSKGQLIVGVKNDVPHYALLDQATGEIKGFEVDVA 69 +AV AL F+ +A LE IK+ G+L + + P + ++ E+ GF+ D+ Sbjct: 8 IAVAALLLASTFTAVSARADDLEKIKAAGELKISMSGQYPPFNFVNDQN-EVVGFDADIG 66 Query: 70 KLLAKSILGDDKKIKLVAVNAKTRGPLLDNGSVDAVIATFTITPERKRIYNFSEPYYQDA 129 K +A+ I G I A + G LL N D V+ + TITPER+++ +F PYY Sbjct: 67 KAIAERI-GVKGTIITTAWDGIIAG-LLTN-KYDTVVGSMTITPEREKVVDFVGPYYHAG 123 Query: 130 IGLLVLKEKKYKSLADMKGANIGVAQAATTKKAIGEAAKKIGIDVKFSEFPDYPSIKAAL 189 + V ++ K +SL D+KG IGV T +K A +K G D++ + P + L Sbjct: 124 RAVFVSEQSKVQSLDDLKGKTIGVTLGETHEK---WAREKGGWDIR--TYKGLPELLLEL 178 Query: 190 DAKRVDAFSVDKSILLGYVDDKSEILPDSFEPQ------SYGIVTKKDDP----AFAKYV 239 A RVDA VD ++ V + E + P + GI +KD+P A K + Sbjct: 179 RAGRVDAIVVDNIPVMVAVKETGEKVRKLNTPDIEGGAVAIGIAIRKDNPELKAAMQKAL 238 Query: 240 DDFVKEHKNEIDALAKKW 257 DD + + + ++ KW Sbjct: 239 DDMLAD--GSYEKISMKW 254 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: 156 Number of extensions: 6 Number of successful extensions: 1 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: 260 Length adjustment: 24 Effective length of query: 235 Effective length of database: 236 Effective search space: 55460 Effective search space used: 55460 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 24 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