Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate 7026928 Shewana3_4057 glutamate-5-semialdehyde dehydrogenase (RefSeq)
Query= BRENDA::Q9Z110 (795 letters) >FitnessBrowser__ANA3:7026928 Length = 415 Score = 252 bits (644), Expect = 2e-71 Identities = 154/416 (37%), Positives = 244/416 (58%), Gaps = 14/416 (3%) Query: 363 VEQQGEMARSGGRMLATLEPEQRAEIINHLADLLTDQREEILLANKKDLEEA-EGRLASP 421 ++Q A R LA L+ + ++ +A L ++ EI AN D+ A + L+ Sbjct: 4 IKQISADAAHAARTLAQLDESLKNTVLLDMARSLREKSYEIQSANLIDVHRATQDNLSPA 63 Query: 422 LLKRLSLSTSKLNSLAIGLRQIAASSQESVGRVLRRTRIAKNLELEQVTVPIGVLLVIFE 481 ++ RL+L+ ++ ++A G+ IAA + VGR + L + ++ VP+GV+ +I+E Sbjct: 64 MVDRLTLNQHRIEAMAQGIETIAALP-DPVGRERFIGKRPNGLSISKMRVPLGVVCMIYE 122 Query: 482 SRPDCLPQVAALAIASGNGLLLKGGKEAAHSNRILHLLTQEALSIHGVKEAIQLV---NT 538 +RP+ AL SGN ++L+GGKEA H+++++ + Q L+ +G+ +A+ V Sbjct: 123 ARPNVTADAGALCFKSGNAVILRGGKEALHTSQVIASILQAVLTAYGLPKALISVIPDPD 182 Query: 539 REEVEDLCRLDKIIDLIIPRGSSQLVRDIQKAAKGIPVMGHSEGICHMYVDSEASVDKVT 598 R + +L + + ID+IIPRG L+ + + + IPV+ H +G+CH+YVD +A+ D Sbjct: 183 RALMLELMQQREFIDVIIPRGGEGLINYVTENSS-IPVIQHFKGVCHLYVDKDANQDIAL 241 Query: 599 RLVRDSKCEYPAACNALETLLIHRDLLRTPLF-DQIIDMLRVEQVKIHAGPKFASYL--- 654 L+ + K + CNALE LL+H+D+ P F ++ L QVKI+A P A+Y Sbjct: 242 DLLLNGKTQRTGVCNALEGLLVHKDI--APRFLPRVAKALAEHQVKINACPPAAAYFDAC 299 Query: 655 TFSPSEVKSLRTEYGDLEVCIEVVDSVQEAIDHIHKYGSSHTDVIVTENEKTAEFFLQHV 714 T+ E EY DLE+ I VDS + A HI K+GS HT+VI T+NE TA F + V Sbjct: 300 TYMAEE--DFGQEYLDLEIAIRQVDSFEVATQHIAKFGSHHTEVICTDNELTAARFQRAV 357 Query: 715 DSACVFWNASTRFSDGYRFGLGAEVGISTSRIHARGPVGLEGLLTTKWLLRGQDHV 770 D++ V NAS+RFSDG GLGAE+GI+T+++HA GP+GLE L T K+L+ G + Sbjct: 358 DASVVMVNASSRFSDGSELGLGAEIGIATTKLHAYGPMGLEALTTEKYLVSGTGQI 413 Lambda K H 0.319 0.134 0.383 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: 684 Number of extensions: 26 Number of successful extensions: 4 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: 795 Length of database: 415 Length adjustment: 36 Effective length of query: 759 Effective length of database: 379 Effective search space: 287661 Effective search space used: 287661 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: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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