Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_086511774.1 BZY95_RS20670 aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >NCBI__GCF_002151265.1:WP_086511774.1 Length = 486 Score = 298 bits (763), Expect = 3e-85 Identities = 181/479 (37%), Positives = 263/479 (54%), Gaps = 10/479 (2%) Query: 22 AFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATF--NSGVWSQLA 79 A I GE+ + + +P GR +A++A C + AV+ AR F + G W++ + Sbjct: 12 ALIGGEWVPTQA--LLDVQTPSSGRTIAQIARCQAEEVMVAVDAARRAFAGSLGEWARWS 69 Query: 80 PAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVY 139 +R L++F D + + LA LE D GKP+ + + DI A+ + DK++ Sbjct: 70 AKRRGEWLLQFGDAIDADHANLAALECADTGKPMSQAEA-DIRACARYFRFYGGGADKLH 128 Query: 140 DEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLT 199 E P L REP GV I+PWN+P + + ALATGNSVVLKP+E + L+ Sbjct: 129 GETLPFDEGFTVLTLREPYGVCAQIIPWNYPAQIFGRCVAAALATGNSVVLKPAEDACLS 188 Query: 200 AIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGES 259 +R+A+LA EAG+P GVLNV+PG G G ALA H +D L FTGS + Q + A + Sbjct: 189 VLRLAELACEAGLPPGVLNVVPGLGREAGAALAAHPAIDHLSFTGSPETGTQ-VAQAAAA 247 Query: 260 NMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFL 319 + + LE GGKSP IVFADA D+ A +A AI N G+ C+AGSRLLVE S + L Sbjct: 248 HHVPVTLELGGKSPQIVFADA-DMDVALDAVVRAIIQNAGQTCSAGSRLLVEASCAEAVL 306 Query: 320 PMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTL-EET 378 +VE + + + G L++ +Q + + +EA DG ++ A G Sbjct: 307 GELVERFSALR-CDAGEANADCGPLINARQKAGLEARLEAAQADGVRVAAQGALAAGAPE 365 Query: 379 GGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDI 438 GG +V P + + + +EE+FGPVL+V F EA+ +AN T +GL AG+WT D Sbjct: 366 GGHFVVPHLLTDIPAGHAVLREELFGPVLAVQVFRDETEALRLANATDFGLCAGVWTRDG 425 Query: 439 SKAHKTARAVRAGSVWVNQYD-GGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIK 496 + + A+ +R+G V++N Y GG + PFGG +SG+GR+K L YT LK IK Sbjct: 426 GRQLRLAKGIRSGQVFINNYGAGGGIELPFGGVGRSGHGREKGFEGLRSYTRLKTVAIK 484 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: 648 Number of extensions: 34 Number of successful extensions: 8 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 24 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