Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate WP_043880120.1 AZC_RS07250 dihydroxy-acid dehydratase
Query= reanno::pseudo5_N2C3_1:AO356_24585 (578 letters) >NCBI__GCF_000010525.1:WP_043880120.1 Length = 571 Score = 502 bits (1293), Expect = e-146 Identities = 268/558 (48%), Positives = 363/558 (65%), Gaps = 6/558 (1%) Query: 9 RSAQWFGTADKNGFMYRSWMKNQGIADHQFHGKPIIGICNTWSELTPCNAHFRQIAEHVK 68 R+ +G + F+ ++++K G +D +PIIGI NT+S+ PC+ + ++ E VK Sbjct: 17 RNLASYGDPGFSLFLRKAFIKAAGYSDDALD-RPIIGITNTFSDFNPCHGNVPRLIEAVK 75 Query: 69 RGVIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEEAIRGNPIDGVVLLTGCDKTT 128 RGV+ AGG P+EFP S ES PT+M RNL +MD EE IR P+D VVL+ GCDKT Sbjct: 76 RGVMLAGGLPMEFPTVSIHESFSNPTSMFLRNLMAMDTEEMIRAQPMDAVVLIGGCDKTV 135 Query: 129 PALLMGAASCDVPAIVVTGGPMLNGKHKGQDIGSGTVVWQLSEQVKAGTITIDDFLAAEG 188 PA LMGA S +VPAI + GPML G HKG+ +G+ T +L Q +AG + ++ G Sbjct: 136 PAQLMGAVSANVPAIQLITGPMLVGHHKGEILGACTDCRRLWGQHRAGHLDAEEMDVLSG 195 Query: 189 GMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGMRAVEMVRED 248 ++ + GTC MGTASTM C+ EALG +LP IPA A R A SG +AV++ Sbjct: 196 RLAPTQGTCMVMGTASTMGCLVEALGIALPWTGTIPATHADRIRAAEASGRQAVQLATHG 255 Query: 249 LKLSKILTKEAFENAIRVNAAIGGSTNAVIHLKAIAGRIGVQLDLDDWTRIGRGMPTIVD 308 +LT AF NA+ V AIGGSTN ++HL AIA R G+ +DLD + IGR +P ++D Sbjct: 256 PTPRDLLTPAAFRNALTVLQAIGGSTNGLVHLAAIARRAGLSVDLDAFDAIGRSVPVLID 315 Query: 309 LQPSGRFLMEEFYYAGGLPAVLRRLGEANLIPNPNALTVNGKSLGENTKDAPIYGQDEVI 368 L+PSG ME F++AGG+P +++ LG+ + +A T++G+++GE A +I Sbjct: 316 LKPSGDHYMEHFHWAGGVPKLMKELGDH---LDRSAPTIDGRTIGEIADAAEEVPGQAII 372 Query: 369 RTLDNPIRADGGICVLRGNLAPLGAVLKPSAATAELMQHRGRAVVFENFDEYKARINDPE 428 R P++ GG+ VLRGNLAP GAV+K SAA+ L++H GRAVVF++ ++ RI+DP Sbjct: 373 RPASAPLKPFGGMAVLRGNLAPGGAVIKHSAASEALLRHTGRAVVFDSVEDMVNRIDDPG 432 Query: 429 LDVDANSILVMKNCGPKGYPGMAEVGNMGLPAKLLAQGVTDMVRISDARMSGTAYGTVVL 488 LDV A+ +LV++N GPKG PGM E G + +P KL GV DMVRISDARMSGTA+GT+VL Sbjct: 433 LDVQADDVLVLRNAGPKGAPGMPEAGYLPIPKKLAQAGVKDMVRISDARMSGTAFGTIVL 492 Query: 489 HVAPEAAAGGPLAAVKEGDWIELDCASGRLHLDIPDAELAARLADLAPPQQL--LVGGYR 546 H+ PEAA GGPL V+ GD I LD A+ + L +PD EL R A+ PP L GY+ Sbjct: 493 HITPEAAVGGPLGLVRSGDTIRLDVAAREIALLVPDEELERRRAEWTPPAHLAEAARGYQ 552 Query: 547 QLYIDHVLQADQGCDFDF 564 LY+ HVLQAD+GCDFDF Sbjct: 553 HLYLTHVLQADEGCDFDF 570 Lambda K H 0.319 0.136 0.409 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: 927 Number of extensions: 40 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: 578 Length of database: 571 Length adjustment: 36 Effective length of query: 542 Effective length of database: 535 Effective search space: 289970 Effective search space used: 289970 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 (21.7 bits) S2: 53 (25.0 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