Align predicted periplasmic glycoside 3-dehydrogenase (EC 1.1.99.13) (characterized)
to candidate Echvi_2281 Echvi_2281 Predicted dehydrogenases and related proteins
Query= reanno::Btheta:351686 (491 letters) >FitnessBrowser__Cola:Echvi_2281 Length = 486 Score = 355 bits (910), Expect = e-102 Identities = 202/467 (43%), Positives = 263/467 (56%), Gaps = 43/467 (9%) Query: 5 SRRKFLKTGAAALAGITIAPSSILGMSHGHVSPTDKLNLAAVGIGGMGHANINNV--KGT 62 SRR FLK A A AG + P +LG G +P+DK+ +A +G GG G ++IN + G Sbjct: 12 SRRAFLKGAATAAAGFYLVPRHVLG-GPGFTAPSDKIVIAGIGAGGKGQSDINAMYQSGH 70 Query: 63 ENIVALCDVDWKYAKGVFDEFPNAKKYWDYRKMYDEMGKSIDGVIIATADHTHAIITADA 122 I LCDVD + A + FP AK Y D+R++ ++ K+ID V ++T DH HA+IT A Sbjct: 71 AEIGYLCDVDDRRAATSRERFPKAKYYKDFRELLEKEHKNIDAVTVSTPDHNHAVITLAA 130 Query: 123 MTMGKHVYCQKPLTHSVYESRLLTKLAASTGVVTQMGNQGASGEGTDLVCEWIWNGEIGE 182 M +GKHVY QKPLTH +YE+R+LT+ A VVTQMGNQG+SG+G + EW G IGE Sbjct: 131 MQLGKHVYVQKPLTHDIYEARMLTEAAEKYKVVTQMGNQGSSGDGVRRMVEWYDAGLIGE 190 Query: 183 VTKVECATDRPIWPQGLNAPEKADRIPNTLNWDLFTGPAKLNPYNNVYHPWNWRGWWDYG 242 TKV C TDRP+WPQG+ PEK P L+WDL+ G A Y + P+NWRGWWDYG Sbjct: 191 ATKVWCWTDRPVWPQGIKWPEKGTTPPKELDWDLWLGTAPYKEYVDNLVPFNWRGWWDYG 250 Query: 243 TGALGDMACHILHQPFRALKLGYPTKVEGSSTLLL----------SACAPQAQHVKMIFP 292 TGALGDMACHI+ PFRAL LGYPT+ E S + C P + HV + F Sbjct: 251 TGALGDMACHIMEPPFRALGLGYPTEAECSVGSVYVGEFQRGYFPDGC-PPSSHVTLKF- 308 Query: 293 ARDNMPKVALPEVEVHWYDGGMMPERPKGFPEGKQLMGPGGGLTIFHGTKDTLICGCYGE 352 MP + ++E HW DGG+ P RP+ +Q MG GG I GTK ++C YG Sbjct: 309 ---KMP--SGKDLEFHWMDGGIQPTRPEELGPNEQ-MGDGGNGVIIEGTKGKMMCSTYGI 362 Query: 353 QPFLLSGRVPNAPKVCRRV------TCSHEMDWVRACKEDKSNRVMPK--ADFSESGPMN 404 P LL + KV + + H WV+AC ++ + + FS +GP+ Sbjct: 363 NPMLLPTSREDGEKVPKTIPRVENGDNGHYAQWVKACVAGHGSKEFKELSSPFSIAGPLT 422 Query: 405 EMVVMGVLAIRLQGLNKTLE--------------WDGANMCFTNIGD 437 E V+MG LAIR + K E WDG NM TN + Sbjct: 423 ESVLMGNLAIRSYDIRKPREDNGFDYPGRGIKLVWDGPNMKVTNFDE 469 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: 794 Number of extensions: 51 Number of successful extensions: 8 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: 491 Length of database: 486 Length adjustment: 34 Effective length of query: 457 Effective length of database: 452 Effective search space: 206564 Effective search space used: 206564 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