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 N515DRAFT_2409 N515DRAFT_2409 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__Dyella79:N515DRAFT_2409 Length = 574 Score = 744 bits (1920), Expect = 0.0 Identities = 369/568 (64%), Positives = 450/568 (79%), Gaps = 3/568 (0%) Query: 12 RSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELAEKVK 71 RSQEW+G + Y+R WLK G P+D+FDGRPVIGI NTWS++TPCN RELAE VK Sbjct: 10 RSQEWFGREGKQGFYYRSWLKGLGLPNDMFDGRPVIGICNTWSELTPCNSSFRELAEHVK 69 Query: 72 AGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLVGCDKTT 131 GV+EAGGFPLE PV S E RPTAM++RNLA++ VEE+IR P+DG VLL+GCDKTT Sbjct: 70 RGVYEAGGFPLEFPVMSLGETQMRPTAMLFRNLASMDVEESIRANPIDGVVLLMGCDKTT 129 Query: 132 PSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEA 191 P+L+MGAAS +LP+I ++GGP L+G +RG+ +GSGT + + SEMV+AGE+ Q EF+EAEA Sbjct: 130 PALMMGAASVNLPTIGLSGGPSLSGNWRGQPIGSGTGVIRMSEMVRAGELAQEEFVEAEA 189 Query: 192 SMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDD 251 M RS G+C TMGTASTMASM EALG++L NAAIP VDSRR +A L+GRRIV+MV +D Sbjct: 190 CMQRSKGSCMTMGTASTMASMVEALGLSLPENAAIPAVDSRRFRLAHLSGRRIVEMVHED 249 Query: 252 LKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVN 311 L+ S+I+T+ AFENAIR NAAIGGSTNAVIHLLA+AGR+G++L+LDDWDR G +P +VN Sbjct: 250 LRMSKILTRAAFENAIRANAAIGGSTNAVIHLLALAGRLGVELALDDWDRLGSHLPCLVN 309 Query: 312 LMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNEDVILP 371 L PSG YLME+F+YAGGLP VL+ + A LH ALT +G T+ D + WN DVI P Sbjct: 310 LKPSGDYLMEDFYYAGGLPAVLREI--APHLHLGALTANGRTLGDNIATAPCWNRDVIRP 367 Query: 372 AEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKINDDNLD 431 E+ L GI VLRGNLAP GAV+KPSAAS HLL H+GRAVVFE+IDD+KA+I+D+ LD Sbjct: 368 IEEPLKREAGIAVLRGNLAPDGAVIKPSAASAHLLQHRGRAVVFENIDDFKARIDDEALD 427 Query: 432 IDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTVVLHT 491 IDE C+MV+KNCGP+GYPGMAEVGNM LPPK+L++GI D+VRISDARMSGTAYGTVVLH Sbjct: 428 IDETCVMVLKNCGPRGYPGMAEVGNMPLPPKLLRRGITDIVRISDARMSGTAYGTVVLHA 487 Query: 492 SPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTSGYAFLHQ 551 SPEAA GG LA+V++GD IELDVP RRLHLD++D+ELARR A W+ P G+A L+ Sbjct: 488 SPEAAAGGNLALVRDGDFIELDVPGRRLHLDLADDELARRRAAWKAPPP-PERGWAKLYV 546 Query: 552 QHVEGADTGADLDFLKGCRGNAVGKDSH 579 HV+ A GADLD L G G+ V DSH Sbjct: 547 DHVQQAHLGADLDILVGGSGSDVAGDSH 574 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: 1171 Number of extensions: 63 Number of successful extensions: 4 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: 574 Length adjustment: 36 Effective length of query: 543 Effective length of database: 538 Effective search space: 292134 Effective search space used: 292134 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