Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate WP_040608878.1 C792_RS0111230 glutamate-5-semialdehyde dehydrogenase
Query= BRENDA::Q941T1 (735 letters) >NCBI__GCF_000330705.1:WP_040608878.1 Length = 423 Score = 249 bits (635), Expect = 3e-70 Identities = 140/414 (33%), Positives = 236/414 (57%), Gaps = 7/414 (1%) Query: 311 EATAREMAVAARDCSRHLQKLSSEERKKILLDIADALEANEDLITSENQADLDLAQDIGY 370 EA + A+ ++ L+KLS++E+ L + LE + I N D++ + G Sbjct: 9 EAIIENLGTKAKHAAKVLRKLSAKEKDAALEAMIGGLENHAGKILEANSKDIENGKKNGL 68 Query: 371 DKSLVARMTIKPGKIKSLAGSIREIADMEDPISHTLKRTEVAKDLVFEKTYCPLGVLLII 430 +LV R+T+ ++ + +R++ ++ DP + + + L K PLGV+ II Sbjct: 69 GDALVERLTLNEERLAGMQDGLRQMTELTDPTTQNEGQWINEQGLKIGKVRVPLGVIGII 128 Query: 431 FESRPDALVQIASLAIRSGNGLLLKGGKEAMRSN-TILHKVITGAIPDVVGKKLIGLVKN 489 +ESRP+ V + L +++GN ++L+GGKEAM SN I+ + G V K+ + L+ + Sbjct: 129 YESRPNVTVDASGLCLKAGNAVILRGGKEAMNSNRAIVEALQEGLSGTAVPKESVQLITD 188 Query: 490 --KDEIADLLKLDDVIDLVIPRGSNKLVSQIKAATKIPVLGHADGICHVYIDKSADMDMA 547 ++ A+ ++ ++ +D +IPRG L+ + +PV+ G CH+YI +SAD +MA Sbjct: 189 PSRELAAEFMQANEYVDCLIPRGGAGLIQTVLKQATVPVIETGTGNCHLYIHESADPEMA 248 Query: 548 KRIVLDAKVDYPAACNAMETLLVHKDLNRTEGLDDLLVELEKEGVVIYGGPVAHDTLK-- 605 K ++++AK + CNA+ETLL+ + E L L L + GV I+G + Sbjct: 249 KSLLINAKTHRVSVCNALETLLIDDSIAEKE-LPALGEALLEAGVAIHGDEKTCSLISEA 307 Query: 606 LPKVDS-FHHEYNSMACTLEFVDDVQSAIDHINRYGSAHTDCIITTDGKAAETFLQQVDS 664 +P ++ + EY ++ VD ++AIDHI+ Y + H+D I TD + + FL +VDS Sbjct: 308 VPATEADYSEEYLGYEIAVKVVDGYEAAIDHIDGYSTGHSDVIAATDYQTIQNFLNEVDS 367 Query: 665 AAVFHNASTRFCDGARFGLGAEVGISTGRIHARGPVGVDGLLTTRCILRGSGQV 718 AAV+ NASTRF DG FG G E+GIST ++HARGP+G++ L + + ++ GSGQ+ Sbjct: 368 AAVYANASTRFTDGEMFGFGGEIGISTQKLHARGPMGLEALTSYKYVVEGSGQI 421 Lambda K H 0.318 0.136 0.385 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: 668 Number of extensions: 29 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: 735 Length of database: 423 Length adjustment: 36 Effective length of query: 699 Effective length of database: 387 Effective search space: 270513 Effective search space used: 270513 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 Jul 26 2024. The underlying query database was built on Jul 25 2024.
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