Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate Ac3H11_1496 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1496 Length = 500 Score = 383 bits (984), Expect = e-111 Identities = 216/474 (45%), Positives = 284/474 (59%), Gaps = 9/474 (1%) Query: 24 INGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAKR 83 I G A+SG P +A+ D AD RAV +A+ F+S VW L PA R Sbjct: 26 IGGVSGPALSGRWLPVTDPATEMVVAEAPDSDAADIARAVASAQRAFDSHVWRGLRPADR 85 Query: 84 KAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIH----WTAEAIDKVY 139 + L R ++L+ ++ +EL+ LETL GK G + +ID+ A+ + W + + Sbjct: 86 EKLLFRLSELIERHADELSALETLQSGKLQGIARAIDVQAGAEFVRYMAGWATKLEGQTL 145 Query: 140 DEVAPTPHDQLGLVTR-EPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPL 198 D P P Q TR EPVGVVGAIVPWNFPL +A WK+ PALA G +VVLKPSE +PL Sbjct: 146 DNSIPIPGPQWVTYTRREPVGVVGAIVPWNFPLAIALWKIAPALAAGCTVVLKPSEDTPL 205 Query: 199 TAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGE 258 TA+R+A LA+EAGIP GVLNV+ G G T G AL H V L FTGST + K ++ +A Sbjct: 206 TALRLAHLALEAGIPEGVLNVVCGRGATAGAALIAHPGVRKLSFTGSTAVGK-VVGHAAV 264 Query: 259 SNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKF 318 NM R LE GGKSP +V DA D A+ A+ I F+QG+VCTA SRLLV RS+ + Sbjct: 265 ENMARFTLELGGKSPAVVMEDA-DPSQVAQGIATGIFFHQGQVCTASSRLLVHRSLYRRV 323 Query: 319 LPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEET 378 L + +G + G+ D T G L V+ +I + +GA L+AGG+R Sbjct: 324 LDELAGIAQGMRIGSGFDAATQFGPLTSKAHFARVMDFIASAKAEGATLVAGGERV--HD 381 Query: 379 GGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDI 438 G +V+PTIF T MR+ +EE+FGPVL+V FD E+A+A ANDTPYGLAA +WT + Sbjct: 382 AGCFVQPTIFADTTAQMRVVREEVFGPVLAVAPFDDVEDAIAAANDTPYGLAASLWTQSL 441 Query: 439 SKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKA 492 S AH+ ++AG VWVN ++ D P GG KQSG GRD A+E +TELK+ Sbjct: 442 SHAHRIVPRLQAGVVWVNAHNVLDAGLPLGGIKQSGTGRDLGRAAVEGFTELKS 495 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: 629 Number of extensions: 27 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: 500 Length adjustment: 34 Effective length of query: 463 Effective length of database: 466 Effective search space: 215758 Effective search space used: 215758 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