Align 4-hydroxy-2-oxovalerate aldolase 2; HOA 2; EC 4.1.3.39; 4-hydroxy-2-keto-pentanoic acid aldolase 2; 4-hydroxy-2-oxopentanoate aldolase 2 (uncharacterized)
to candidate N515DRAFT_0574 N515DRAFT_0574 2-isopropylmalate synthase
Query= curated2:B2HI25 (347 letters) >FitnessBrowser__Dyella79:N515DRAFT_0574 Length = 535 Score = 60.5 bits (145), Expect = 1e-13 Identities = 68/271 (25%), Positives = 114/271 (42%), Gaps = 40/271 (14%) Query: 7 VRITDTSLRDGSHHKRHQFIKEEVGAIVAALDAAGVPVIEVTHGDGLGGSSFNYGFSKTP 66 VRI DT+LRDG + + AL+A GV V+E GF + Sbjct: 22 VRIFDTTLRDGEQAPGFGMDRRAKLRMAHALEALGVDVMEA-------------GFPQAS 68 Query: 67 EQELIKLA--AQTAKEAKIAFL---MLPGVGTKEDIKEAQDNGGSICRIATHCTEADVSI 121 + +A A+ + + + L + T EA + RI + + + Sbjct: 69 PDDFAAVADIAKAVRHSTVCALARCQAADIDTAGRALEAAQHS----RIHVFLSTSPLHR 124 Query: 122 QH-FGLARELGLETVGFLM-----MAHTIA----------PEKLAAQARIMADAGCQCVY 165 +H G++++ ++T + + H + P+ LA AG V Sbjct: 125 EHKLGMSKQQVIDTAIAAVERARALCHEVEFSAEDAMRTEPDYLAEVFSAAIAAGATTVN 184 Query: 166 VVDSAGALVLDGVADRVAALVAELGEDAQVGF--HGHENLGLGVANSVEAVRAGAKQIDG 223 D+ G + +A+R A L + +V F H H++LG+ VANS+ AV AGA+QI+ Sbjct: 185 APDTVGYVTPAEIAERFAYLRKHVKGAERVVFSSHCHDDLGMAVANSLAAVSAGARQIEC 244 Query: 224 SVRRFGAGAGNAPVEALIGVFDKIGVKTGID 254 ++ G AGNA +E ++ G G+D Sbjct: 245 TINGIGERAGNASLEEVVMALRVRGPYFGVD 275 Lambda K H 0.319 0.136 0.389 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: 430 Number of extensions: 22 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 347 Length of database: 535 Length adjustment: 32 Effective length of query: 315 Effective length of database: 503 Effective search space: 158445 Effective search space used: 158445 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: 51 (24.3 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