Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate N515DRAFT_0379 N515DRAFT_0379 Acyl-CoA reductase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__Dyella79:N515DRAFT_0379 Length = 476 Score = 197 bits (501), Expect = 7e-55 Identities = 144/463 (31%), Positives = 224/463 (48%), Gaps = 24/463 (5%) Query: 38 ECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAKRKAKLIRFADLLRKN 97 + L G+ +VA D +A+ A A + Q P +R+A L + Sbjct: 22 DVLDKYSGKVATRVAVPDAKATEQAI--AAAVKAAEPMRQFKPWERQAVLQHCVQRFTER 79 Query: 98 VEELALLETLDMGKPIGDSSS-----IDIPGAA--QAIHWTAEAIDKVYDEVAPTPHDQL 150 +ELA ++ GKPI DS+ I+ G A +A+ E I+ E+A + Sbjct: 80 RDELAYALCVEAGKPIKDSAGEVTRLIETFGIAAEEAVRTNGETINL---EIAKRLNGYH 136 Query: 151 GLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIRIAQLAIEA 210 G R P+G V I P+NFPL + K+ PA+A G VLKP+E++P+ A+ I ++ E Sbjct: 137 GYTRRVPLGPVSFITPFNFPLNLVAHKVAPAIAAGCPFVLKPAERTPIGALIIGEVLAET 196 Query: 211 GIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMKRIWLEAGG 270 +P G ++L G L L FTGS +I L AG K++ LE GG Sbjct: 197 DLPKGAFSILNLDGKH-ASPLVEDPRFKLLSFTGS-QIGWDLKTRAGH---KKVTLELGG 251 Query: 271 KSPNIVFAD-APDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMVVEALKGW 329 + IV AD P L E + G+ C + R+ S+ D+ +V A+KG Sbjct: 252 NAACIVDADQLPRLDHVIERLVFGAFYQSGQSCISVQRIYAHESLYDELKKRLVAAVKGL 311 Query: 330 KPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGTYVEPTIFD 389 K G+P +T +G ++D + +IE K G K+L GGKR G +E T+ + Sbjct: 312 KAGDPKKKETFLGPMIDEAAAERLHGWIEEARKGGGKVLCGGKRK-----GPMLEATLME 366 Query: 390 GVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKAHKTARAVR 449 V ++ ++E+FGP + F + +EA+A+ ND+ YGL AGI+T ++ A + + Sbjct: 367 NVRGDAKVNRQEVFGPFALLAPFKSLDEAIAMTNDSDYGLQAGIFTDSLANAMRAWNELE 426 Query: 450 AGSVWVNQYDGGDM-TAPFGGFKQSGNGRDKSLHALEKYTELK 491 G V VN + P+GG K SG GR+ +A+E TE++ Sbjct: 427 QGGVIVNDVPSFRVDNMPYGGVKLSGAGREGVRYAIEDMTEIR 469 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: 557 Number of extensions: 29 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: 476 Length adjustment: 34 Effective length of query: 463 Effective length of database: 442 Effective search space: 204646 Effective search space used: 204646 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