Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_029134446.1 A3GO_RS0117140 aldehyde dehydrogenase family protein
Query= BRENDA::Q72IB9 (516 letters) >NCBI__GCF_000428045.1:WP_029134446.1 Length = 480 Score = 231 bits (590), Expect = 3e-65 Identities = 168/481 (34%), Positives = 247/481 (51%), Gaps = 22/481 (4%) Query: 41 YIGGEWVDTKE--RMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDR 98 YI G+WVD + + +NPS E T A G+A+ +AA+ AA AF W +E R Sbjct: 8 YINGQWVDPIKPVELEVINPST-EEPCATIALGGQADTDAAVAAARNAFGDWSQSDREQR 66 Query: 99 SRLLLKAAALMRRRKRELEATLVYEVGKNWVEA-SADVAEAIDFIEYYARAALRYRYPAV 157 LL K A + + R E+ + E+G A +A I I+ + RA + + Sbjct: 67 LALLEKLAEIYQARSNEMAEAISSEMGAPISLAKTAQCGAGIWHIKNFIRALKTFEFER- 125 Query: 158 EVVPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVGA 217 + P+ D P+G +I PWN+P+ T ++ +A G T++ KP+E + + Sbjct: 126 RLGPHAPNDR-ILLEPVGVCGLITPWNWPMNQVTLKVIPALATGCTLVLKPSEISPLSAM 184 Query: 218 KVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLAP 277 E+ +AGFPPGV N + G G VG+ L HP I+FTGS G+ I ++A Sbjct: 185 LFAEMIDQAGFPPGVFNLVNGDGAGVGSQLTAHPDVDMISFTGSTRAGIAISKSAADTV- 243 Query: 278 GQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEP 337 KR +E GGK A +V AD + G + + GQ C+A +R+++ + Y+ Sbjct: 244 -----KRVSLELGGKGANLVFADADENAIKRG-LRHCFNNSGQSCNAPTRMLVQRPLYQQ 297 Query: 338 VLERVLKRAERLSVG-PAEENPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGK-RLEG 394 +E + AE +V A E +GPVVS Q K+ I+ G +EG +LV GG R EG Sbjct: 298 AVETAAQLAEGTAVDHSANEGRHIGPVVSQAQYDKIQRLIQQGTDEGARLVAGGPGRPEG 357 Query: 395 --EGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSR 452 GYF+ PTVF +V +IA+EEIFGPVLS+ EA+ +ANDT YGLT + ++ Sbjct: 358 IDRGYFVRPTVFADVGQDMQIAREEIFGPVLSITPFDSEEEAITIANDTVYGLTNYIQTQ 417 Query: 453 KREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEMKAV 512 + R+ G + N GA PFGG+K SG N + G + L FLE+KAV Sbjct: 418 DSARAKRVARQLRSGMVEINGHSPGA---GSPFGGYKQSG-NGREGGVWGLEEFLEVKAV 473 Query: 513 A 513 + Sbjct: 474 S 474 Lambda K H 0.319 0.137 0.403 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: 548 Number of extensions: 33 Number of successful extensions: 6 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: 516 Length of database: 480 Length adjustment: 34 Effective length of query: 482 Effective length of database: 446 Effective search space: 214972 Effective search space used: 214972 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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