Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate BPHYT_RS23175 BPHYT_RS23175 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__BFirm:BPHYT_RS23175 Length = 497 Score = 531 bits (1369), Expect = e-155 Identities = 269/497 (54%), Positives = 352/497 (70%), Gaps = 5/497 (1%) Query: 1 MNFHHLAYWQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDID 60 M+ A+WQDKA +L+IE R FI+GEY A TF+ + P+ LAK+A + D+D Sbjct: 1 MDKKSFAFWQDKAATLSIEGRAFIDGEYRDAEGGRTFDCLSPIDGKLLAKVADSGAADVD 60 Query: 61 RAMSAARGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDD 120 A++AAR F+ G WS +P +RKAVL + A + H +ELALLETLD GKPI + D Sbjct: 61 AAVAAARRAFDSGVWSGLNPRQRKAVLLRWAASIREHMDELALLETLDAGKPIADTTSVD 120 Query: 121 IPGAARAIRWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGP 180 +PGAA + W+AEAIDK+ GEVA H L ++ REP+GV+AA+VPWNFP+L+ WK GP Sbjct: 121 VPGAAYCVEWFAEAIDKIGGEVAPADHHLLGLVTREPIGVVAAVVPWNFPILMASWKFGP 180 Query: 181 ALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAI 240 ALAAGNSV+LKPSEKSPL+AIRLA LA +AG+P GV NVV G G E G+ L+ H D+D + Sbjct: 181 ALAAGNSVVLKPSEKSPLTAIRLAQLALDAGIPAGVFNVVPGAG-EPGKLLALHQDVDCL 239 Query: 241 AFTGSTRTGKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQ 300 AFTGST GK +++ AG SN+KRVWLE GGKS NIV DCPD+ +AA+A A IFYN G+ Sbjct: 240 AFTGSTNVGKLIMQYAGQSNLKRVWLELGGKSPNIVMPDCPDMDRAANAAAGAIFYNMGE 299 Query: 301 VCIAGTRLLLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREG 360 +C AG+RLL+ I D F+ L A+++ PG+PLDP T+MG ++D + V +I G Sbjct: 300 MCTAGSRLLVHRDIKDVFIDKLIAAARSYTPGNPLDPDTSMGAIVDKVQLERVLGYIEAG 359 Query: 361 ESKGQLLLDGRNAGLAAA---IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQL 417 ++ +LLL G I PTIF A ++REEIFGPVL V F + E+A+++ Sbjct: 360 RAEAKLLLGGARVKEDTGGFYIEPTIFEIPGSGAKVAREEIFGPVLSVITFDTVEEAIRI 419 Query: 418 ANDSQYGLGAAVWTRDLSRAHRMSRRLKAGSVFVNNYND-GDMTVPFGGYKQSGNGRDKS 476 ANDS+YGL AAVWT +L+ AH +SR+L+AG+V+VN Y++ GDM PFGGYKQSGNGRDKS Sbjct: 420 ANDSEYGLAAAVWTSNLTTAHEVSRKLRAGTVWVNCYDEGGDMNFPFGGYKQSGNGRDKS 479 Query: 477 LHALEKFTELKTIWISL 493 LHALEK+TELK+ + L Sbjct: 480 LHALEKYTELKSTLVRL 496 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: 693 Number of extensions: 25 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: 495 Length of database: 497 Length adjustment: 34 Effective length of query: 461 Effective length of database: 463 Effective search space: 213443 Effective search space used: 213443 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