Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate 3609638 Dshi_3021 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__Dino:3609638 Length = 485 Score = 301 bits (770), Expect = 4e-86 Identities = 187/477 (39%), Positives = 268/477 (56%), Gaps = 17/477 (3%) Query: 20 NRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSS 79 + + I G + A+ T E +DP PLA+IARG + +IDRA++AAR + GDW S Sbjct: 14 DEILIGGVWQRCAD--TLEVIDPSDGTPLAQIARGGAAEIDRAVAAARAALD-GDWGRMS 70 Query: 80 PAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVY 139 +R L +L L+ + LA +E D GKP+ + R D AR + +Y A DKV Sbjct: 71 ATERGRCLTRLGALVAGEVDRLAEMEARDVGKPLSQA-RADALALARYLEFYGGAADKVM 129 Query: 140 GEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLS 199 GE S +REP GV IVPWN+P+ + +G ALA GN+ +LKP+E + L+ Sbjct: 130 GETIPYQSGYTVYTLREPHGVTGHIVPWNYPMQIIGRSVGAALAMGNACVLKPAEDACLT 189 Query: 200 AIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDS 259 A+ A LA+ AGLP G LNVVTG G EAG ALS H +D ++FTGS G ++ A Sbjct: 190 ALAFARLAEAAGLPPGALNVVTGLGAEAGAALSDHPGVDHLSFTGSVPVGAEVQATAA-R 248 Query: 260 NMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFL 319 ++ V LE GGKS IVFAD DL A G N GQ C A R+L++ + D Sbjct: 249 HITPVTLELGGKSPQIVFADA-DLDAALPFLVKGGVQNAGQTCSAAARILVQTDVFDAVA 307 Query: 320 ALLKQQAQNWQPGHPL-DPATTMGTLIDCAHADSVHSFIREGE-----SKGQLLLDGRNA 373 + + + G L DPA +G LI V + + + + + G LL + Sbjct: 308 DRMAEAYRALTVGPALSDPA--VGPLISPKQKARVSAMLAQAQPDQILATGHLLPEAPEG 365 Query: 374 GLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRD 433 G + P + + + L+++EIFGPV ++ RF +E++A+ LAN +++GL A +WTRD Sbjct: 366 G--CYVLPHLLGGIAADHPLAQQEIFGPVQILMRFETEQEAIALANGTEFGLVAGIWTRD 423 Query: 434 LSRAHRMSRRLKAGSVFVNNYN-DGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTI 489 +R RM +RL+AG VFVN Y G + +PFGG +SG+GR+K AL F++LKT+ Sbjct: 424 GARQMRMPKRLRAGQVFVNTYGAGGGVELPFGGVGKSGHGREKGFEALFGFSQLKTV 480 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: 558 Number of extensions: 28 Number of successful extensions: 7 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: 485 Length adjustment: 34 Effective length of query: 461 Effective length of database: 451 Effective search space: 207911 Effective search space used: 207911 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 17 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