Align tagaturonate epimerase (EC 5.1.2.7) (characterized)
to candidate WP_003470005.1 J416_RS09955 hypothetical protein
Query= BRENDA::Q9WYS1 (481 letters) >NCBI__GCF_000359605.1:WP_003470005.1 Length = 504 Score = 355 bits (911), Expect = e-102 Identities = 202/476 (42%), Positives = 283/476 (59%), Gaps = 18/476 (3%) Query: 16 VYEKSYREKDSLSFFLTKEEEGKILVVAGEKAPEGLSFFKKQRAEGVSFF-FCERNHENL 74 VY S+ E + K K++V AG F+ E + C HEN Sbjct: 26 VYTPSFEEHAGSQVVMVKSGTEKMIVAAGAG-----ELFEALSGEDIGKGKVCPLTHENR 80 Query: 75 EVLRKYFPDLKPVRAGLR-ASFGTGDRLGITTPAHVRALKDSGLFPIFAQQSVRENERTG 133 VL ++F P G A+ G GDRLGI +P H+ +K+ + PI AQQS+RE Sbjct: 81 LVLNQFFSYTAPQAFGTDIATMGLGDRLGIASPGHIDTVKERNVKPILAQQSIRELTLLN 140 Query: 134 RTWRDVLDDATWGVFQEGYSEGFGADADHVKRPEDLVSAAREGFTMFTIDPSDHVRN-LS 192 RT D+LD A + VFQEGY +G+GADADH+K D+ A + GF+ T+D S+ +RN + Sbjct: 141 RTMTDILDAAAFAVFQEGYKDGYGADADHIKLESDIEHALQLGFSFLTLDCSEQIRNDVE 200 Query: 193 KLTEKERNEKFEEILRKER--IDRIYLGKKYSVLGEKIEFDEKNLRDAALVYYDAIAHVD 250 T E +F + ++R YL + ++V +I FD+ NL LVY +AI ++ Sbjct: 201 SQTSDEIQNEFASLSDEKRAYFSNYYLDQTFNVHERQISFDQANLAKNVLVYGEAIDFME 260 Query: 251 MMYQI-LKDETPDFDFEVSVDETETPTSPLFHIFVVEELRRRGVEFTNLALRFIGEWEKG 309 +Y L+ D DFE+S+DETET TSP H FV EELRRRGV+ +LA RF GE++KG Sbjct: 261 HVYHTYLQSLDRDVDFEISIDETETVTSPEAHFFVAEELRRRGVKVESLAPRFCGEFQKG 320 Query: 310 IDYKGDLAQFEREIKMHAEIARMFEGYKISLHSGSDKFSVYPAFASATGGLFHVKTAGTS 369 IDY GD+ QFE+E+K HA+IA+ F GYK+S+HSGSDKFSV+P T GL H+KTAGT+ Sbjct: 321 IDYIGDMDQFEKELKEHADIAKHF-GYKLSIHSGSDKFSVFPIIGKYTDGLLHIKTAGTN 379 Query: 370 YLEAVKVISMVNPELFREIYRCTLDHFEEDRKSYHISADLSKVPEVEKVKDEDLPGLFED 429 +LEAV+V++ NP+L+R ++ +HFEE K YH++ DL V +++ D+ LP Sbjct: 380 WLEAVRVVAQENPDLYRRMHVYAEEHFEETLKYYHVTPDLDSVTPLKEQPDDQLPEYMNH 439 Query: 430 INVRQLIHVTYGSVL--KDAS----LKERLFKTLEQNEELFYETVAKHIKRHVDLL 479 RQL HVTYG +L KD + ++ F TL E+ + + +A HI RH+DLL Sbjct: 440 DAARQLFHVTYGILLTAKDDAGNDLFRDEFFDTLLNKEDAYRQALAHHIGRHLDLL 495 Lambda K H 0.320 0.138 0.398 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: 742 Number of extensions: 40 Number of successful extensions: 5 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: 481 Length of database: 504 Length adjustment: 34 Effective length of query: 447 Effective length of database: 470 Effective search space: 210090 Effective search space used: 210090 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 24 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