Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_043765072.1 U743_RS01785 aldehyde dehydrogenase family protein
Query= BRENDA::Q72IB9 (516 letters) >NCBI__GCF_000733765.1:WP_043765072.1 Length = 506 Score = 217 bits (552), Expect = 9e-61 Identities = 168/480 (35%), Positives = 241/480 (50%), Gaps = 40/480 (8%) Query: 34 FGRHYPLYIGGEWV--DTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWK 91 F Y +IGG+WV ++ + +++P ++ A++ A+ E AL+AA A W Sbjct: 15 FKSRYDNFIGGDWVAPESGKYFDNVSPVTGGKIC-EIARSEAADVEKALDAAHAARARWA 73 Query: 92 DWPQEDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEAS-ADVAEAIDFIEYYARAAL 150 + +RS +L A M L ++ GK E++ ADV AID Y+A A+ Sbjct: 74 NTSTTERSNILNAIAQRMEDNLEALAQAETWDNGKAVRESTVADVPLAIDHFRYFA-GAI 132 Query: 151 RYRYPAVEVVPYPGEDNES----FYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIA 206 R + ++ ++ D ++ F+ PLG I PWNFP+ + + +A GN V+ Sbjct: 133 RAQEGSISMI-----DEQTVAYHFHEPLGVVGQIIPWNFPLLMAVWKLAPALAAGNCVVI 187 Query: 207 KPAEDAVVVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGL 266 KPAE E+ + PPGV+N + G G E G L PR FTG G Sbjct: 188 KPAEQTPASILHWMEMIADL-LPPGVINIVNGFGLEAGKPLASSPRIAKAAFTGETTTGR 246 Query: 267 KIYE-AAGRLAPGQTWFKRAYVETGGK------DAIIVDETADFDLAAEGVVVSAYGFQG 319 I + AA L P +E GGK + ++ ++ A FD A EG V+ A QG Sbjct: 247 MIMQYAAQNLIP-------VTLELGGKSPNVFFEDVMREDDAYFDKAIEGFVLFALN-QG 298 Query: 320 QKCSAASRLILTQGAYEPVLERVLKRAERLSVG-PAEENPDLGPVVSAEQERKVLSYIEI 378 + C+ SR ++ + ++ +ER LKR E + +G P + +G S+EQ K+LSY +I Sbjct: 299 EVCTCPSRALIQESIFDRFMERALKRVEAIQMGDPLSMDTMMGAQASSEQMEKILSYFDI 358 Query: 379 GKNEGQLVLGG---KRLEGE---GYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFA 432 GK EG VL G +L+GE GY+I PTVF K R+ QEEIFGPV+SV KD A Sbjct: 359 GKQEGAEVLTGGGRAQLDGELANGYYIKPTVFRG-HNKMRVFQEEIFGPVVSVTTFKDEA 417 Query: 433 EALEVANDTPYGLTGGVYSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSG 492 EALE+ANDT YGL GV+SR R G ++ N A FGG+K SG Sbjct: 418 EALEIANDTLYGLGAGVWSRDANICYRMGRGIQAGRVWTN--CYHAYPAHAAFGGYKQSG 475 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: 584 Number of extensions: 38 Number of successful extensions: 8 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: 506 Length adjustment: 35 Effective length of query: 481 Effective length of database: 471 Effective search space: 226551 Effective search space used: 226551 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