Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate GFF4232 Psest_4305 NAD-dependent aldehyde dehydrogenases
Query= reanno::WCS417:GFF5420 (497 letters) >FitnessBrowser__psRCH2:GFF4232 Length = 497 Score = 854 bits (2206), Expect = 0.0 Identities = 419/497 (84%), Positives = 461/497 (92%) Query: 1 MTTLTRADWEQRAKDLKIEGRAYINGEYTAAVSGDTFECISPVDGRLLATVASCDAADAQ 60 M TLT ADW+QRA+DL IEGRA+I GEY AA G F+CISPVDGR+LA VASC+ ADA+ Sbjct: 1 MPTLTLADWQQRARDLHIEGRAFIQGEYCAAADGGQFDCISPVDGRVLAQVASCEQADAE 60 Query: 61 RAVENARATFNSGVWSRLAPAKRKSAMLRFAALLKANAEELALLETLDMGKPISDSLNID 120 RAV +ARA F++G WSRLAPAKRK+ ++RFA LL+AN EELALLETLDMGKPI DSL +D Sbjct: 61 RAVASARAAFDAGSWSRLAPAKRKAVLIRFADLLEANREELALLETLDMGKPIGDSLAVD 120 Query: 121 VPGAANALSWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGP 180 +PGAA AL WSGEAIDKIYDEVAATPHDQLGLVTREPVGVV AIVPWNFPLMMACWKLGP Sbjct: 121 IPGAARALRWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVAAIVPWNFPLMMACWKLGP 180 Query: 181 ALSTGNSVILKPSEKSPLTAIRIAALAVEAGIPKGVFNVLPGYGHTVGNALALHMDVDTL 240 AL+TGNSV+LKPSEKSPLTAIRIA LA++AGIP GV NVLPGYGHTVG ALALHMDVDTL Sbjct: 181 ALATGNSVVLKPSEKSPLTAIRIAQLAIDAGIPAGVLNVLPGYGHTVGKALALHMDVDTL 240 Query: 241 VFTGSTKIAKQLLIRSGESNMKRVWLEAGGKSPNIVFADAPDLQAAAESAAGAIAFNQGE 300 VFTGST++AKQL+I +GESNMKRVWLEAGGKSPNIVFADAPDLQAAA++AAGAIAFNQGE Sbjct: 241 VFTGSTRVAKQLMIYAGESNMKRVWLEAGGKSPNIVFADAPDLQAAAQAAAGAIAFNQGE 300 Query: 301 VCTAGSRLLVERSIKDKFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAG 360 VCTAGSRLLVERSI+++FLP+V+EALKGWKPGNPLDPATNVGALVDTQQ+NTVL YI+AG Sbjct: 301 VCTAGSRLLVERSIRERFLPMVVEALKGWKPGNPLDPATNVGALVDTQQLNTVLGYIDAG 360 Query: 361 HADGAKLVAGGKRTLEETGGTYVEPTIFDGVTNAMKIAKEEIFGPVLSVITFDSAEEAVA 420 GA+++ GG+RTLEETGG YVEPTIFDGV NAM+IA+EEIFGPVLSVITFDSAEEAVA Sbjct: 361 RQAGAQVLIGGQRTLEETGGLYVEPTIFDGVDNAMRIAQEEIFGPVLSVITFDSAEEAVA 420 Query: 421 IANDTIYGLAAAVWTADISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS 480 IANDT YGLAAAVWTAD+SKAH TA+ALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS Sbjct: 421 IANDTPYGLAAAVWTADLSKAHRTARALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS 480 Query: 481 LHAFDKYTELKATWIKL 497 LHAFDKYTELKATWI+L Sbjct: 481 LHAFDKYTELKATWIQL 497 Lambda K H 0.316 0.132 0.386 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: 858 Number of extensions: 20 Number of successful extensions: 2 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: 497 Length of database: 497 Length adjustment: 34 Effective length of query: 463 Effective length of database: 463 Effective search space: 214369 Effective search space used: 214369 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 (21.6 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