Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate CCNA_01554 CCNA_01554 D-mannonate oxidoreductase
Query= BRENDA::O08355 (493 letters) >FitnessBrowser__Caulo:CCNA_01554 Length = 482 Score = 299 bits (766), Expect = 1e-85 Identities = 172/478 (35%), Positives = 253/478 (52%), Gaps = 9/478 (1%) Query: 1 MKLNKQNLTQLAPEVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWSI 60 ++LN + + P V +P Y + G+ H G G FHRAHQA+Y D L+ W + Sbjct: 11 LRLNATSYPGVVPGVAIPTYDRDKLQIGVVHFGPGAFHRAHQAHYFDQLL--AHDPRWGV 68 Query: 61 CGVGLRSEDRKARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAEDSAQALIDKLA 120 C V L+S RD L QD L+TL +L +T R++GSI ++L+A + ++ +LA Sbjct: 69 CAVSLKSPG--VRDALKPQDGLYTLAQLDA--ETTFRIVGSILEVLVAPEDPPSVFARLA 124 Query: 121 SPEIRIVSLTITEGGYCIDDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAG 180 +P R+V+LT+TE GY + + G +H P I HDLA+P P++ G++ L +R AAG Sbjct: 125 APTTRLVTLTVTEKGYTLSANGGLDESH-PDIVHDLANPREPRSAVGYLVEGLRRRFAAG 183 Query: 181 IPAFTVMSCDNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAMVDRITPMTSTAH 240 + + V++CDNL NG + A++A+AA + L WI FP MVD ITP T A Sbjct: 184 LAPYAVVACDNLADNGWRLKAAVVAYAAKLDESLAAWIDREGRFPRTMVDSITPATDDAL 243 Query: 241 RLQLHDEHGIDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLN 300 R + G++DAWP+ E F QWV+ED P VGV TDDV +E K+ LLN Sbjct: 244 RARTLAATGLEDAWPIQREAFAQWVVEDVLPADGPDLASVGVIMTDDVRGFERAKLRLLN 303 Query: 301 GSHLALTYLGFLKGYRFVHETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVD 360 G H L Y+G L+G+ V E ++DP A M D+ P L P G+DL Y ++ Sbjct: 304 GVHSTLAYVGILRGHETVFEAVSDPTLAALASDMMAKDIIPTLTPPRGLDLQAYADAILG 363 Query: 361 RFSNQAIADQLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDEN 420 RF N I L ++ DGS K P + T+ + GR ER A+ +AAW ++ + Sbjct: 364 RFRNPEIRHLLAQIAWDGSQKLPFRILGTLTETLEAGRSIERLAVPLAAWMRFVALRAKA 423 Query: 421 GVSYTIPDPRAEFCQGLVSDDALISQ--RLLAVEEIFGTAIPNSPEFVAAFERCYGSL 476 G + P GL + + LA++ +F ++ P FV+A E+ Y L Sbjct: 424 GEAIVDPLQDRLLALGLAATGEASADVAAFLALDSVFPASLAGDPRFVSALEKAYADL 481 Lambda K H 0.321 0.137 0.414 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: 626 Number of extensions: 32 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: 493 Length of database: 482 Length adjustment: 34 Effective length of query: 459 Effective length of database: 448 Effective search space: 205632 Effective search space used: 205632 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