Align α-ketoglutaric semialdehyde dehydrogenase subunit (EC 1.2.1.26) (characterized)
to candidate PfGW456L13_3585 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26)
Query= metacyc::G1G01-1343-MONOMER (525 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3585 Length = 525 Score = 865 bits (2235), Expect = 0.0 Identities = 432/524 (82%), Positives = 471/524 (89%) Query: 1 MPLTGNLLIGQRPVTGSRDAIRAIDPTTGQTLEPAYLGGTGEHVAQACALAWAAFDAYRE 60 M LTGN+LIGQ+ + G+R+AIR IDP T LEPAY GG+GEHV QACALAW+A D+YR Sbjct: 1 MTLTGNMLIGQQAIAGNREAIRGIDPATDLPLEPAYHGGSGEHVEQACALAWSALDSYRA 60 Query: 61 TSLEQRAEFLEAIATQIEALGDALIDRAVIETGLPKARIQGERGRTCTQLRTFARTVRAG 120 TSLE RAEFLE IA++IEALGD LIDRAV ETGLP+ RIQGERGRTC QLRTFA TVRAG Sbjct: 61 TSLEARAEFLETIASEIEALGDELIDRAVAETGLPRPRIQGERGRTCQQLRTFALTVRAG 120 Query: 121 EWLDVRIDSALPERQPLPRADLRQRQVALGPVAVFGASNFPLAFSVAGGDTASALAAGCP 180 EWLDVR+DSALPERQPLPR DLRQRQV LGPVAVFGASNFPLAFSVAGGDTASALAAGCP Sbjct: 121 EWLDVRVDSALPERQPLPRPDLRQRQVPLGPVAVFGASNFPLAFSVAGGDTASALAAGCP 180 Query: 181 VVVKAHSAHPGTSELVGQAVAQAVKQCGLPEGVFSLLYGSGREVGIALVSDPRIKAVGFT 240 V+VKAH AHPGTSELVG+A+A+AVK CGL EGVFSLL+GSGREVGIALV+DPRIKAVGFT Sbjct: 181 VIVKAHGAHPGTSELVGRALARAVKLCGLHEGVFSLLFGSGREVGIALVTDPRIKAVGFT 240 Query: 241 GSRSGGMALCQAAQARPEPIPVYAEMSSINPVFLFDAALQARAEALAQGFVASLTQGAGQ 300 GSRSGG+ALC AAQARPEPIPVYAEMSSINPV LF AALQ+RAEALAQGFVASLTQGAGQ Sbjct: 241 GSRSGGIALCNAAQARPEPIPVYAEMSSINPVLLFPAALQSRAEALAQGFVASLTQGAGQ 300 Query: 301 FCTNPGLVIARQGPALQRFITAAAGYVQQGAAQTMLTPGIFSAYQAGIAALADNPHAQAI 360 FCTNPGLVIARQGP L+RFI +AA +Q+ AQTMLTPGIF AY+AG+ ALA++ HA+ + Sbjct: 301 FCTNPGLVIARQGPDLERFIQSAAQLLQRSPAQTMLTPGIFKAYEAGVGALAEHAHAETV 360 Query: 361 TSGQAGQGPNQCQAQLFVTQAEAFLADPALQAEVFGAASLVVACTDDEQVRQVAEHLEGQ 420 G G+ PNQCQA LFVTQA FLADPALQAE+FGAASL+V C DEQ+RQV EHLEGQ Sbjct: 361 AVGLKGETPNQCQAHLFVTQASEFLADPALQAEMFGAASLIVQCASDEQIRQVIEHLEGQ 420 Query: 421 LTATLQLDEADIDSARALLPTLERKAGRILVNGWPTGVEVCDAMVHGGPFPATSDARTTS 480 LTATL LD+AD++SARALLP LERKAGR+LVNGWPTGVEVCDAMVHGGPFPATSDARTTS Sbjct: 421 LTATLHLDDADVESARALLPILERKAGRLLVNGWPTGVEVCDAMVHGGPFPATSDARTTS 480 Query: 481 VGTAAILRFLRPVCYQDVPDALLPQALKHGNPLQLRRLLDGKRE 524 VGTAAILRFLRPVCYQD PDALLP ALKHGNPLQLRRLLDG+RE Sbjct: 481 VGTAAILRFLRPVCYQDFPDALLPAALKHGNPLQLRRLLDGQRE 524 Lambda K H 0.319 0.134 0.391 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: 982 Number of extensions: 30 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: 525 Length of database: 525 Length adjustment: 35 Effective length of query: 490 Effective length of database: 490 Effective search space: 240100 Effective search space used: 240100 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