Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_022949182.1 H035_RS0111795 aldehyde dehydrogenase family protein
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_000421465.1:WP_022949182.1 Length = 506 Score = 338 bits (867), Expect = 3e-97 Identities = 199/484 (41%), Positives = 279/484 (57%), Gaps = 16/484 (3%) Query: 23 FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82 +I G + A + FE + PVT P ++AR + DI++A+ AA + W +SPA Sbjct: 22 YIGGHWIAPVNGQYFENITPVTGTPFCEVARSTAEDIEKALDAAHAA--KDAWGKTSPAG 79 Query: 83 RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142 R +L K+AD ME E LA+ ET D GKPIR +L DIP AA R++A AI V Sbjct: 80 RADLLLKIADRMEQQLEMLAVAETWDNGKPIRETLAADIPLAADHFRYFASAIRTQESSV 139 Query: 143 ATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIR 202 + +A EP+GV+ I+PWNFPLL+ WKL PALAAGN V+LKP+E++P S + Sbjct: 140 CEIDADTIAYHFHEPLGVVGQIIPWNFPLLMASWKLAPALAAGNCVVLKPAEQTPASILV 199 Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262 L L + +P GV+NVV GFG EAG+ L+R + I +AFTG T TG+ +++ A N+ Sbjct: 200 LMELIGDL-IPPGVVNVVNGFGVEAGKPLARSSRIAKVAFTGETTTGRLIMQYA-SQNLI 257 Query: 263 RVWLEAGGKSANIVFADCPDLQQA----ASATAAGIFYNQGQVCIAGTRLLLEESIADEF 318 V LE GGKS N+ F D Q A A NQG+VC +R LL+ SI D+F Sbjct: 258 PVTLELGGKSPNLFFEDVTAKQDTFVDKALEGFASFALNQGEVCTCPSRALLQASIYDDF 317 Query: 319 LALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKG-QLLLDGRNAGLAA 377 + ++ + + G+PLD T +G + + S+I +G + L+ G A L Sbjct: 318 IHRALERVKAIRQGNPLDTETMIGAQASAEQMEKILSYIDIARQEGTECLIGGERAQLQG 377 Query: 378 A------IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWT 431 I PTIF + + +EEIFGPVL VT F EE+AL++AND+ YGLGA VWT Sbjct: 378 ELAGGYYIQPTIFKGHN-QMRVFQEEIFGPVLAVTTFRDEEEALEIANDTLYGLGAGVWT 436 Query: 432 RDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWI 491 RD++ A+RM R ++AG V+ N Y+ FGGYKQSG GR+ L+ + + K + + Sbjct: 437 RDMNTAYRMGRGIQAGRVWTNCYHLYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKNLLV 496 Query: 492 SLEA 495 S +A Sbjct: 497 SYDA 500 Lambda K H 0.317 0.133 0.389 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: 563 Number of extensions: 26 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: 495 Length of database: 506 Length adjustment: 34 Effective length of query: 461 Effective length of database: 472 Effective search space: 217592 Effective search space used: 217592 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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