Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate AZOBR_RS27005 AZOBR_RS27005 cytochrome C biogenesis protein CcmE
Query= SwissProt::Q92RN6 (256 letters) >FitnessBrowser__azobra:AZOBR_RS27005 Length = 259 Score = 139 bits (349), Expect = 8e-38 Identities = 87/255 (34%), Positives = 133/255 (52%), Gaps = 11/255 (4%) Query: 11 LRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSL-ALCEKVAAQTGQAPHFIQ 69 +R+R +VTG +GIG A ARQG V + + LC ++AAQ+G + Sbjct: 1 MRNRNAVVTGSTTGIGLATARELARQGCHVMLNGFGDRAEIDRLCTEIAAQSGTTIVYSG 60 Query: 70 ADLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRHLFFM 129 ADL E RA +A A LG + +LVNNA A+ ++ WD L+VNL F Sbjct: 61 ADLSRPEEARAMMADAAAALGPIDILVNNAGVQHVAAVHEFPDDKWDLLLAVNLSAAFHT 120 Query: 130 CQAVAPHMQRQGGGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLGPDNIRVN 189 +A P M+ + G IVN +S+ ++ P PAY K GIIGLTKS+A ++ I N Sbjct: 121 IKAALPAMRERRWGRIVNTASVLGMVGAPHKPAYVATKHGIIGLTKSVAIEVAEHGITCN 180 Query: 190 AILPGMIVT--------ERQRRLWLTEESI--ARMQERQCLKRMLVADDLVGPCLFLASD 239 A+ PG ++T ++ + L EE + A +R R++ +++ FL SD Sbjct: 181 AVCPGTVLTPIIEKQIAQQAQVTGLPEERVLQAVFLDRMPTGRLIPPEEVAAAIAFLCSD 240 Query: 240 SSAAMTAQAMIIDGG 254 ++A++T A+ +DGG Sbjct: 241 AAASITGTAIPVDGG 255 Lambda K H 0.321 0.133 0.377 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: 138 Number of extensions: 6 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: 256 Length of database: 259 Length adjustment: 24 Effective length of query: 232 Effective length of database: 235 Effective search space: 54520 Effective search space used: 54520 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 (21.9 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