Align predicted periplasmic 3-ketoglycoside hydrolase (DUF1080) (characterized)
to candidate CA265_RS02410 CA265_RS02410 hypothetical protein
Query= reanno::Caulo:CCNA_01705 (281 letters) >FitnessBrowser__Pedo557:CA265_RS02410 Length = 269 Score = 176 bits (446), Expect = 5e-49 Identities = 99/237 (41%), Positives = 136/237 (57%), Gaps = 6/237 (2%) Query: 43 WRSLFDGKTLNGWTAKVARHPVGENYRQTFVADQGVIRVSYAGYDRFDNQFGHLFHKTPF 102 W +LF+GK + W K+ H N+ TF + G I+V Y Y F++QFGHL++KTPF Sbjct: 29 WITLFNGKDIKDWNVKIHHHDYNVNFGNTFRVEDGTIQVRYDQYGDFNDQFGHLYYKTPF 88 Query: 103 SAYRLRFSYRFLTEGGLPDTPGWARANSGIMFHSQSAESMTVDQPFPVSIEFQLLGKDGD 162 S Y L+ YRF+ E P + NSG+MFHSQ ++M +Q +P+SIE Q LG D Sbjct: 89 SYYHLKLKYRFVGE-LQKGAPSYTLRNSGVMFHSQDPKTMPKEQDWPISIEMQFLGGLSD 147 Query: 163 -KPRPTGAVCTPGITITIDGAKVKEHCTPPANGPTIANGTWVQAELEVLPSGEITQKING 221 +PRPTG +C+PG I +G+K HC + T WV AEL V+ + ING Sbjct: 148 GRPRPTGNMCSPGTEIFYNGSKYPGHCL-DSKSKTYDGDQWVSAELIVMGDSIVKHIING 206 Query: 222 VVVHRYAGAALDPDDTVAGGAKPYILARGAQPVTGGYIALQSEGAPLEFKDIEIQEL 278 V +Y+ + VA P I G + +T G+IALQSEG P++FKDI+I EL Sbjct: 207 DTVLQYSKPQI--GGGVANRFDPKIKIDG-KALTEGFIALQSEGQPVDFKDIQIMEL 260 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: 247 Number of extensions: 19 Number of successful extensions: 5 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: 269 Length adjustment: 25 Effective length of query: 256 Effective length of database: 244 Effective search space: 62464 Effective search space used: 62464 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