Align predicted periplasmic glycoside 3-dehydrogenase (EC 1.1.99.13) (characterized)
to candidate Echvi_0565 Echvi_0565 Predicted dehydrogenases and related proteins
Query= reanno::Btheta:351686 (491 letters) >FitnessBrowser__Cola:Echvi_0565 Length = 488 Score = 295 bits (754), Expect = 3e-84 Identities = 186/485 (38%), Positives = 257/485 (52%), Gaps = 46/485 (9%) Query: 5 SRRKFLKTGAAALAGITIAPSSILGMSHGHVSPTDKLNLAAVGIGGMGHANINN--VKGT 62 SRR F+K A A + + I P +LG G +P+D+LN+AA+G GG G ++I N V G Sbjct: 12 SRRNFIKNAALASSAL-IVPRHVLG-GVGFTAPSDQLNIAAIGAGGKGASDIKNASVNGR 69 Query: 63 ENIVALCDVDWK-YAKGVFDEFPNAKKYWDYRKMYDEMGKSIDGVIIATADHTHAIITAD 121 E +VALCDVD+ A FPNAK Y D+R+M E K ID V I+T DH H A Sbjct: 70 ERVVALCDVDFSGSASQSVKNFPNAKLYADFREML-EKEKDIDAVTISTPDHVHGPAAAF 128 Query: 122 AMTMGKHVYCQKPLTHSVYESRLLTKLAASTGVVTQMGNQGASGEGTDLVCEWIWNGEIG 181 AM GKHVY QKP+TH++ E+RLLT++A VVTQMGNQG S +LV +WI + ++G Sbjct: 129 AMERGKHVYVQKPMTHNIREARLLTQMAREQKVVTQMGNQGGSNPLLNLVQQWIDSDKLG 188 Query: 182 EVTKVECATDRPIWPQGLNAPE-KADRIPNTLNWDLFTGPAKLNPYNNVYHPWNWRGWWD 240 +++KVE T+RP+WPQG P+ + P+ L WDL+ GP+ PY HP+NWRGWWD Sbjct: 189 KISKVEIWTNRPVWPQGNAFPQPDPSKKPDDLAWDLWLGPSPKIPYTPNLHPFNWRGWWD 248 Query: 241 YGTGALGDMACHILHQPFRALKLGYPTKVEGSSTLLLSAC---------APQAQHVKMIF 291 YGTGALGD+ CH++ P+R L L YP E S + + P + + + F Sbjct: 249 YGTGALGDVGCHLVDIPYRTLGLHYPKSAECSVGAVYTKMWTPDYHPEGCPASSFISLKF 308 Query: 292 PARDNMPKVALPEVEVHWYDGGMMPERPKGFPEGKQLMG--PGGGLTIFHGTKDTLICGC 349 A + + +E+ W DGG+ P P P + G G+ I G K + Sbjct: 309 DATEK----SKSPIEMTWSDGGIRPAHPDIIPADHDIGGTDSANGVLII-GEKGIISTNI 363 Query: 350 YGEQP-----FLLSGRVPNAPKV--CRRVTCSHEMDWVRACKEDKSNRVMPK--ADFSES 400 P +L G P+ H+ WV ACK ++ + + F + Sbjct: 364 NDSSPLMPKLYLNDGTTEFGPQTEDFPEPEYGHQRKWVDACKAGFGSKEHNELTSSFDYA 423 Query: 401 GPMNEMVVMGVLAIRLQGL-------------NKTLEWDGANMCFTNIGD-NETLRTCIK 446 GPM E V+MG LAIR L K L WDG NM TN+ + N+ + + Sbjct: 424 GPMTETVLMGNLAIRSYMLRRENSNGGMEYFGRKKLLWDGDNMQITNLEEANQYVGRTYR 483 Query: 447 DGFTI 451 DG+ + Sbjct: 484 DGWKV 488 Lambda K H 0.319 0.136 0.444 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: 728 Number of extensions: 40 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 491 Length of database: 488 Length adjustment: 34 Effective length of query: 457 Effective length of database: 454 Effective search space: 207478 Effective search space used: 207478 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 (21.8 bits) S2: 52 (24.6 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