Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 5208453 Shew_0965 methylmalonate-semialdehyde dehydrogenase (RefSeq)
Query= reanno::WCS417:GFF5420 (497 letters) >FitnessBrowser__PV4:5208453 Length = 496 Score = 216 bits (550), Expect = 1e-60 Identities = 150/468 (32%), Positives = 237/468 (50%), Gaps = 37/468 (7%) Query: 23 YINGEYT--AAVSGDTFECISPVDGRLLATVASCDAADAQRAVENARATFNSGVWSRLAP 80 YING++T +A S FE P G A V+ A + A+E A+ G WS + P Sbjct: 7 YINGQHTQPSARSAAVFE---PATGEHKANVSLASALEVDAAIELAKKAH--GPWSEMTP 61 Query: 81 AKRKSAMLRFAALLKANAEELALLETLDMGKPISDSLNIDVPGAANALSWSGEAIDKIYD 140 R + +F AL++AN +ELA + T + GK + D+ + G ++ + Sbjct: 62 LNRARILFKFKALVEANMDELAAMITREHGKVLDDAKGEIIRGL------------EVVE 109 Query: 141 EVAATPH-------DQLG-----LVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSV 188 PH +Q+G + +GVV I P+NFP+M+ W A++ GN+ Sbjct: 110 FACGIPHLLKGEHTEQVGGGVDAWTLNQSLGVVAGIAPFNFPVMVPMWMFPIAIAAGNTF 169 Query: 189 ILKPSEKSPLTAIRIAALAVEAGIPKGVFNVLPGYGHTVGNALALHMDVDTLVFTGSTKI 248 I+KPSEK P + +R+A L EAG+P GVFNV+ G V + L H D+ + F GST I Sbjct: 170 IMKPSEKDPTSVMRMAELLTEAGLPDGVFNVVNGDKEAV-DTLLTHKDIQAVSFVGSTPI 228 Query: 249 AKQLLIRSGESNMKRVWLEAGGKSPNIVFADAPDLQAAAESAAGAIAFNQGEVCTAGSRL 308 A + + ++ ++ KRV G K+ ++ DA DL A + GA + GE C A S + Sbjct: 229 A-EYIYQTAAAHGKRVQALGGAKNHMLLMPDA-DLDQAVSALMGAAYGSAGERCMAISVV 286 Query: 309 LVERSIKDKFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHADGAKLV 368 L + D + ++ ++ K GN L+ +G L+ Q ++ V SY++ G ++GA L+ Sbjct: 287 LAVGEVGDALVEKLLPQIQALKVGNGLEGEMEMGPLISAQHLDKVRSYVDTGVSEGASLL 346 Query: 369 AGGKR--TLEETGGTYVEPTIFDGVTNAMKIAKEEIFGPVLSVITFDSAEEAVAIANDTI 426 A G++ + G ++ +FD VT M I KEEIFGPVL+++ EA+ + N+ Sbjct: 347 ADGRQLTVADHEQGYFLGGCLFDHVTPEMTIYKEEIFGPVLTIVRVKDYAEALTLINEHE 406 Query: 427 YGLAAAVWTADISKAHLTAKALRAGSVWVNQYDGGDMT-APFGGFKQS 473 +G A++T A ++ G V VN M FGG+K+S Sbjct: 407 FGNGTAIFTQSGEAARHFCHHVQVGMVGVNVPIPVPMAFHSFGGWKRS 454 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: 536 Number of extensions: 30 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: 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