Align predicted periplasmic 3-ketoglycoside hydrolase (DUF1080) (characterized)
to candidate CA265_RS14585 CA265_RS14585 hypothetical protein
Query= reanno::Caulo:CCNA_01705 (281 letters) >FitnessBrowser__Pedo557:CA265_RS14585 Length = 276 Score = 181 bits (460), Expect = 1e-50 Identities = 102/243 (41%), Positives = 135/243 (55%), Gaps = 19/243 (7%) Query: 43 WRSLFDGKTLNGWTAKVARHPVGENYRQTFVADQGVIRVSYAGYDRFDNQFGHLFHKTPF 102 W +LF+GK L W K+A+H EN+ TF GV++VSY GY+ FD Q+GH+F+K PF Sbjct: 26 WINLFNGKDLKDWNIKIAKHEYKENFANTFRVKNGVMKVSYDGYNEFDKQYGHIFYKKPF 85 Query: 103 SAYRLRFSYRFL---TEGGLPDTPGWARANSGIMFHSQSAESMTVDQPFPVSIEFQLLGK 159 SAY L+ +YRF+ +GG GWA NSG M H Q +M DQ FP+SIE Q+LG Sbjct: 86 SAYLLKVTYRFVGDQAKGG----EGWATRNSGAMLHCQDPATMLKDQDFPISIEAQILGG 141 Query: 160 DGDKPRPTGAVCTPGITITIDGAKVKEHCTPPANGPTIANGTWVQAELEVLPSGEITQKI 219 DG+ R T VCTPG I +G HC + T A WV AE VL + I Sbjct: 142 DGEHERHTSNVCTPGTLINYNGKLFTGHCL-DSKSKTYAGDQWVTAEFLVLGDSVVKHII 200 Query: 220 NGVVVHRYAGAALDPDDTVAGGA----KPYILARGAQPVTGGYIALQSEGAPLEFKDIEI 275 G VV Y + GG+ P + G + +T GYI+LQSE P+EFK +++ Sbjct: 201 AGEVVLEYT------KPQIGGGSVSNFDPKVKIDG-KALTSGYISLQSESHPIEFKTVQL 253 Query: 276 QEL 278 +L Sbjct: 254 YDL 256 Lambda K H 0.318 0.137 0.427 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: 248 Number of extensions: 14 Number of successful extensions: 3 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: 281 Length of database: 276 Length adjustment: 25 Effective length of query: 256 Effective length of database: 251 Effective search space: 64256 Effective search space used: 64256 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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