Align predicted periplasmic glycoside 3-dehydrogenase (EC 1.1.99.13) (characterized)
to candidate CA265_RS15365 CA265_RS15365 oxidoreductase
Query= reanno::Btheta:351686 (491 letters) >FitnessBrowser__Pedo557:CA265_RS15365 Length = 485 Score = 314 bits (804), Expect = 5e-90 Identities = 185/463 (39%), Positives = 249/463 (53%), Gaps = 37/463 (7%) Query: 5 SRRKFLKTGAAALAGITIAPSSILGMSHGHVSPTDKLNLAAVGIGGMGHANINNV--KGT 62 +RR F+KT A A A I P +LG G+++P+D+L +A +G+GG G +++N G Sbjct: 12 NRRDFIKTTAIAAAAFMIVPRHVLG-GPGYLAPSDRLLVAGIGVGGKGQSDLNMFYKSGK 70 Query: 63 ENIVALCDVDWKYAKGVFDEFPNAKKYWDYRKMYDEMGKSIDGVIIATADHTHAIITADA 122 +I LCDVD + A FP AK Y D+R+M D+ K+ D V ++T DH HAI A Sbjct: 71 ADIAFLCDVDDRRAANSVKAFPKAKYYKDWREMLDKEHKNFDAVSVSTPDHNHAIQALAA 130 Query: 123 MTMGKHVYCQKPLTHSVYESRLLTKLAASTGVVTQMGNQGASGEGTDLVCEWIWNGEIGE 182 M +GKHVY QKPLTH +YE+R+LT A VVTQMGNQGAS +G + EW G IG+ Sbjct: 131 MQLGKHVYVQKPLTHDIYEARILTAAAKKYKVVTQMGNQGASNDGPRQMKEWYEAGLIGD 190 Query: 183 VTKVECATDRPIWPQGLNAPEKADRIPNTLNWDLFTGPAKLNPYNNVYHPWNWRGWWDYG 242 V V TDRP+WPQG+ P K IP L+W+L+ G A + + P+NWRGWWDYG Sbjct: 191 VHTVYAWTDRPVWPQGIPRPTKKAEIPAELDWNLWLGTAPEKDFIDKLVPFNWRGWWDYG 250 Query: 243 TGALGDMACHILHQPFRALKLGYPTKVEGSSTLL---------LSACAPQAQHVKMIFPA 293 TGALGDM CH++ PF L L Y +VE S + P + HV + FP Sbjct: 251 TGALGDMGCHLIEAPFSVLNLKYAKEVEASVGSVYVDEFKRGYFPESCPPSSHVTLKFP- 309 Query: 294 RDNMPKVALPEVEVHWYDGGMMPERPKGFPEGKQLMGPGGGLTIFHGTKDTLICGCYGEQ 353 + N K +V +HW DGG+ PERP+ E + G GG T+F GTK ++ Y Sbjct: 310 KTNKTK---GDVTLHWMDGGIQPERPEEL-EANETFGDGGNGTLFIGTKGKMMSETYSAN 365 Query: 354 PFLL----SGRVPNAPKVCR--RVTCSHEMDWVRACKEDKSNRVMPKADFSESGPMNEMV 407 P LL + + APK R H WV A + + + F +GP+ E + Sbjct: 366 PKLLPLSKNKDIKVAPKYTRVPDGANGHYKQWVEAAIAGYGKQEV-SSPFEIAGPLTEAL 424 Query: 408 VMGVLAIRLQGLNKTLE-------------WDGANMCFTNIGD 437 +M LAIR + KT+ WD NM TN + Sbjct: 425 LMANLAIRSFDIQKTVNGKTTYPGRYTKMLWDNDNMKVTNFDE 467 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: 715 Number of extensions: 38 Number of successful extensions: 7 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: 485 Length adjustment: 34 Effective length of query: 457 Effective length of database: 451 Effective search space: 206107 Effective search space used: 206107 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