Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate HSERO_RS05710 HSERO_RS05710 aldehyde dehydrogenase
Query= reanno::WCS417:GFF5420 (497 letters) >FitnessBrowser__HerbieS:HSERO_RS05710 Length = 486 Score = 311 bits (797), Expect = 3e-89 Identities = 193/471 (40%), Positives = 267/471 (56%), Gaps = 10/471 (2%) Query: 23 YINGEYTAAVSGDTFECISPVDGRLLATVASCDAADAQRAVENARATFNSGVWSRLAPAK 82 YI+G++ + ++P + +A +AAD +AV+ AR + W+ +P + Sbjct: 19 YIDGKWQPPQGSERAAVVAPATEERVCEIALGNAADVDQAVQAARRAIPA--WAATSPLE 76 Query: 83 RKSAMLRFAALLKANAEELALLETLDMGKPISDSLNIDVPGAANALSWSGEAIDKIYDEV 142 R + + R ALL +E A TL+MG PIS + VP AA L A D + D Sbjct: 77 RAALLGRVHALLLERSELFAQALTLEMGAPISYARTAHVPLAAEHLR---VARDNLADYP 133 Query: 143 AATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEKSPLTAIR 202 P +V REP+GV I PWN+P+ K+GPAL+ G +V+LKPSE SPL+A+ Sbjct: 134 FIRPRGTTAIV-REPIGVCALITPWNWPIYQITAKVGPALAAGCTVVLKPSELSPLSALL 192 Query: 203 IAALAVEAGIPKGVFNVLPGYGHTVGNALALHMDVDTLVFTGSTKIAKQLLIRSGESNMK 262 A + EAG+P GVFN++ G G VG AL+ H VD + TGST+ A L+ ++ +K Sbjct: 193 FAEIVHEAGVPAGVFNLVNGSGAEVGAALSAHPQVDMISITGSTR-AGVLVAQAAAVTVK 251 Query: 263 RVWLEAGGKSPNIVFADAPDLQAAAESAAGAIAFNQGEVCTAGSRLLVERSIKDKFLPLV 322 RV E GGKSPN+V DA DL+ A A N G+ C+A +RL+V R+ + L Sbjct: 252 RVAQELGGKSPNLVLPDA-DLERAIPPGVAAALRNMGQSCSAPTRLIVPRAALARVHELA 310 Query: 323 IEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHADGAKLVAGGK-RTLEETGGT 381 + L K G+P D AT G L + Q V IEAG DGA+L+AGG R G Sbjct: 311 LATLAQMKVGDPNDAATTHGPLANRAQFLRVQQMIEAGLQDGARLLAGGPGRPDGLAQGY 370 Query: 382 YVEPTIFDGVTNAMKIAKEEIFGPVLSVITFDSAEEAVAIANDTIYGLAAAVWTADISKA 441 Y PTIF V M IA+EEIFGPVL+++ +D+ EEA+AIANDT+YGL A V D + Sbjct: 371 YARPTIFSEVHTDMVIAQEEIFGPVLAILPYDTVEEAIAIANDTVYGLGAHVQGRDKDQV 430 Query: 442 HLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKA 492 A +++G V +N Y D APFGG+KQSGNGR+ + ++Y E+KA Sbjct: 431 RAVAARIQSGQVHLN-YPAWDPQAPFGGYKQSGNGREYGVEGMEEYMEVKA 480 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: 545 Number of extensions: 18 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: 497 Length of database: 486 Length adjustment: 34 Effective length of query: 463 Effective length of database: 452 Effective search space: 209276 Effective search space used: 209276 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