Align L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized)
to candidate RR42_RS33305 RR42_RS33305 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__Cup4G11:RR42_RS33305 Length = 579 Score = 550 bits (1416), Expect = e-161 Identities = 268/579 (46%), Positives = 380/579 (65%), Gaps = 3/579 (0%) Query: 1 MKKKAEWPRKLRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCN 60 M + + P LRS W+ HR + GY D + RP+I I+NTWSD+ PC+ Sbjct: 1 MTSRKKTPETLRSARWFAPDDLRSSGHRSRIMQMGYSPDEWLDRPIIAIINTWSDINPCH 60 Query: 61 GHLRELAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDG 120 H ++ + VK G+ +AGGFP+E+P S SE+ +PT M+YRN+ A+ EE IR P+DG Sbjct: 61 SHFKQRVDDVKRGILQAGGFPIELPAISLSESAVKPTTMLYRNMLAMEAEELIRSHPVDG 120 Query: 121 CVLLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGE 180 VL+ GCDKTTP LLMGA+S +P+I V GPML G ++G +GSG+ WKF + +AG Sbjct: 121 AVLMGGCDKTTPGLLMGASSAGVPAIYVPAGPMLRGNWKGNVLGSGSDAWKFWDERRAGN 180 Query: 181 MTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLT 240 +++ E++ E ++RS GTC TMGTASTM ++AEA+GM L G ++IP D+ M Sbjct: 181 ISKTEWIGIEGGIARSHGTCMTMGTASTMTAIAEAIGMTLPGASSIPAADANHIRMCSEA 240 Query: 241 GRRIVQMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWD 300 GRRIV MV +DL P I T+ +FENAI A+G STNA+IH++A+A R G D+ L+D+D Sbjct: 241 GRRIVDMVWEDLTPQRIQTRASFENAIAVAMAMGCSTNAIIHVIAMARRAGHDIGLEDFD 300 Query: 301 RCGRDVPTIVNLMPSG-KYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVK 359 + R VP I N+ PSG KYLME+FFYAGGLP ++ R+ + L+ DALTV+G T+ + + Sbjct: 301 KTSRHVPVIANIRPSGDKYLMEDFFYAGGLPALMNRISDK--LNLDALTVTGRTLGENIA 358 Query: 360 DVVNWNEDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDID 419 +N+DVI E AL G + VL+GN+AP G V+KPSA H G A+VF+D Sbjct: 359 GAEVYNDDVIRTKENALYQEGALAVLKGNIAPDGCVIKPSACEKRFFKHTGPALVFDDYP 418 Query: 420 DYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARM 479 K + D+LD+ + I++++N GP+G PGM E G + +P K++++G+ DM+R+SDARM Sbjct: 419 SMKEAVERDDLDVTADHILILRNAGPQGGPGMPEWGMLPIPKKLVQQGVRDMLRMSDARM 478 Query: 480 SGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNH 539 SGT+YG +LH SPE+ +GGP A+V+ GDMI +D+ R +HL++SDEELARR A W P Sbjct: 479 SGTSYGACILHVSPESYIGGPFALVRTGDMISVDIDRRSIHLEVSDEELARRKAAWTPPP 538 Query: 540 DLPTSGYAFLHQQHVEGADTGADLDFLKGCRGNAVGKDS 578 GY ++ +H+ A+ G D DFL+ G G+ S Sbjct: 539 PRFGRGYGWMFSKHIRQANDGCDFDFLQTDFGAPTGEPS 577 Lambda K H 0.318 0.135 0.408 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: 1062 Number of extensions: 41 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: 579 Length of database: 579 Length adjustment: 36 Effective length of query: 543 Effective length of database: 543 Effective search space: 294849 Effective search space used: 294849 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 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