Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 7025959 Shewana3_3107 methylmalonate-semialdehyde dehydrogenase [acylating] (RefSeq)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_805 (497 letters) >FitnessBrowser__ANA3:7025959 Length = 496 Score = 218 bits (556), Expect = 3e-61 Identities = 152/469 (32%), Positives = 236/469 (50%), Gaps = 39/469 (8%) Query: 23 YINGEYTDAVSGETFECISPVDGRLLGKIASCDAADAQRAVENARATFNSGVWSRLAPTK 82 Y+NGE+T A S + E P G G+++ + A+ A++ F++ WS++ P Sbjct: 7 YVNGEHT-AASTRSQEIFEPATGECRGQVSLASRDEVSAAIAIAKSAFDT--WSQVTPLN 63 Query: 83 RKSTMIRFAGLLKQHAEELALLETLDMGKPISDSLYIDVPGAAQALSWSGEAID--KIYD 140 R + +F L++QH +ELA L TL+ GK + D+ GE I ++ + Sbjct: 64 RARVLFKFKALVEQHMDELAQLITLEHGKVLDDA--------------RGELIRGLEVVE 109 Query: 141 EVAATPH-------DQLG-----LVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSV 188 PH +Q+G + +GVV I P+NFP+M+ W A++ GN+ Sbjct: 110 FACGIPHLLKGEHTEQVGGGVDAWSVNQALGVVAGIAPFNFPVMVPMWMFPIAIACGNTF 169 Query: 189 ILKPSEKSPLTAIRIAELAVEAGIPKGVLNVLPGYGHTVGKALALHNDVDTLVFTGSTKI 248 I+KPSEK P +RIAEL +AG+P GV NV+ G V L+ H D+ + F GST I Sbjct: 170 IMKPSEKDPSAVMRIAELLTQAGLPAGVFNVVNGDKEAVDTLLS-HEDIQAVSFVGSTPI 228 Query: 249 AKQLLIYSGES-NMKRVWLEAGGKSPNIVFADAPNLQDAAEAAAGAIAFNQGEVCTAGSR 307 A+ IYS S + KRV G K+ ++ DA +L A A GA + GE C A S Sbjct: 229 AE--YIYSTASKHGKRVQALGGAKNHMLLMPDA-DLDQAVSALMGAAYGSAGERCMAISV 285 Query: 308 LLVERSIKDKFLPLVIEALKAWKPGNPLDPATNVGALVDTQQMNTVLSYIESGHADGARL 367 +L + DK + ++ ++ K GN L P +G L+ Q + V ++++G +GA L Sbjct: 286 VLAVGDVGDKLVDKLLPQIQQLKVGNGLTPEMEMGPLISRQHLAKVTEFVDAGVKEGATL 345 Query: 368 VAGGKR--TLQETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIEFDSAEEAIAIANDT 425 V G++ G ++ +FD V+ M+I +EEIFGPVLS++ A+A+ N Sbjct: 346 VVDGRQLTVADHQQGYFLGACLFDNVTPEMRIYREEIFGPVLSIVRVKDYASALALINQH 405 Query: 426 PYGLAAAVWTADISKAHLTARALRAGSVWVNQYDGGDMT-APFGGFKQS 473 +G A++T A ++ G V VN M FGG+K+S Sbjct: 406 EFGNGTAIFTQSGEAARHFCHHVQVGMVGVNVPIPVPMAFHSFGGWKRS 454 Lambda K H 0.316 0.132 0.390 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: 546 Number of extensions: 30 Number of successful extensions: 5 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: 496 Length adjustment: 34 Effective length of query: 463 Effective length of database: 462 Effective search space: 213906 Effective search space used: 213906 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