Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate Pf1N1B4_4277 Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27)
Query= reanno::pseudo6_N2E2:Pf6N2E2_515 (500 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4277 Length = 500 Score = 917 bits (2370), Expect = 0.0 Identities = 453/500 (90%), Positives = 473/500 (94%) Query: 1 MSDAPVVGHYLNGHVQDHDSTRFSNVFNPATGAVQARVALAEPGTVDAAVASALAAFPAW 60 MSDA V+GHY++G VQD S RFSNVFNPATG++QARV LA TVD AVASAL AFPAW Sbjct: 1 MSDAQVIGHYIDGQVQDCGSERFSNVFNPATGSIQARVGLASQKTVDDAVASALKAFPAW 60 Query: 61 SEQSSLRRSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPN 120 SEQSSLRRSRVMFKFKELLDRHH+ELA+IISREHGKV SDA GEVTRGIEIVEYACGAPN Sbjct: 61 SEQSSLRRSRVMFKFKELLDRHHNELAEIISREHGKVFSDAKGEVTRGIEIVEYACGAPN 120 Query: 121 LLKTDFSDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSER 180 LLKTDFSDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALV GNCFILKPSER Sbjct: 121 LLKTDFSDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVTGNCFILKPSER 180 Query: 181 DPSASLLMARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQG 240 DPSASLLMA+LLTEAGLPDGVFNVVQGDK AVDALLQHPDIEAISFVGSTPIAEYIHQQ Sbjct: 181 DPSASLLMAKLLTEAGLPDGVFNVVQGDKAAVDALLQHPDIEAISFVGSTPIAEYIHQQA 240 Query: 241 TAHGKRVQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDEL 300 T+ GKRVQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAV VGDVGD+L Sbjct: 241 TSRGKRVQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVTVGDVGDQL 300 Query: 301 IAKLLPRIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRSFKVPG 360 IAKLLPRIDQLK+GNG Q +DMGPLVTAEHKAKVEGFI GVA+GA+LIVDGR+FKVPG Sbjct: 301 IAKLLPRIDQLKVGNGMQGDSDMGPLVTAEHKAKVEGFIGEGVAQGAQLIVDGRNFKVPG 360 Query: 361 AEQGFFVGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTR 420 AE GFFVGATLFD VT EMSIYQQEIFGPVLGIVRVPDFA+AVALINAHEFGNGVSCFT Sbjct: 361 AENGFFVGATLFDNVTTEMSIYQQEIFGPVLGIVRVPDFASAVALINAHEFGNGVSCFTS 420 Query: 421 DGGIARAFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSV 480 DGGIAR+FAR+IKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEG+RFYSRYKSV Sbjct: 421 DGGIARSFARNIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGIRFYSRYKSV 480 Query: 481 MQRWPDSIAKGPEFSMPTAQ 500 MQRWPDSIAKGPEFSMPTA+ Sbjct: 481 MQRWPDSIAKGPEFSMPTAK 500 Lambda K H 0.321 0.137 0.415 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: 877 Number of extensions: 23 Number of successful extensions: 1 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: 500 Length of database: 500 Length adjustment: 34 Effective length of query: 466 Effective length of database: 466 Effective search space: 217156 Effective search space used: 217156 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 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