Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate Pf6N2E2_3131 4-aminobutyraldehyde dehydrogenase (EC 1.2.1.19)
Query= SwissProt::Q9H2A2 (487 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3131 Length = 474 Score = 315 bits (806), Expect = 3e-90 Identities = 171/462 (37%), Positives = 265/462 (57%), Gaps = 11/462 (2%) Query: 28 YDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQERSRVLNQVADLLEQSLEEF 87 ++PS G V + + + +++AAV++A AF +WS P++RS +L ++AD +E EE Sbjct: 22 FNPSLGRVLVEINEASEAQVDAAVRSADAAFEAWSQVPPKDRSLLLLKLADAIEAHGEEL 81 Query: 88 AQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSECTQMDHLGCMHYTVRAPVGV 147 A+ ES + GK L+ A +IP FRFFA +S + G R PVGV Sbjct: 82 AKLESDNCGKPLSAALNDEIPAIADVFRFFAGASRCMSGSAGGEYLPGHTSMIRRDPVGV 141 Query: 148 AGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVTAWMLCKLLDKAGVPPGVVNIV 207 I+PWN PL ++ WKIAPA+AAGNTV+ KPSE T +TA L +L + P GV+N++ Sbjct: 142 IASIAPWNYPLMMVAWKIAPALAAGNTVVLKPSEQTPLTALRLAELASEI-FPAGVLNVI 200 Query: 208 FGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKKLSLELGGKNPAIIFEDAN 267 FG G VG LV+HP+V ++S TGS T I ++ K++ +ELGGK P IIF+DA+ Sbjct: 201 FGRGQTVGNPLVTHPKVRMVSLTGSIATGSNIISSTSDSVKRMHMELGGKAPVIIFDDAD 260 Query: 268 LDECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFLKRFVEATRKWKVGIPSDPLVSIG 327 +D + F N G+ C RI+ Q+ IY +F+++ A K G+ + P +G Sbjct: 261 IDAAVEGIRTFGFYNAGQDCTAACRIYAQQGIYEQFVEKLGAAVGSIKYGLQTAPDTEMG 320 Query: 328 ALISKAHLEKVRSYVKRALAEG--AQIWCGEGVDKLSLPARNQAGYFMLPTVITDIKDES 385 LI+ H ++V ++V+RA+A+ I G+ VD G+F PTV+ D + + Sbjct: 321 PLITAQHRDRVAAFVERAIAQPHIRLITGGKAVD--------GNGFFFEPTVLADAQQDD 372 Query: 386 CCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAATVWSSNVGRVHRVAKKLQSGLVWT 445 + E+FGPV V F E +V+ AN+ YGLA++VW++++GR HR++ +LQ G W Sbjct: 373 EIVRREVFGPVVSVTSFLDEAQVLAWANDSDYGLASSVWTADIGRAHRLSARLQYGCTWV 432 Query: 446 NCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTITVKH 487 N + +P GG K SG G++ + + +T ++ + KH Sbjct: 433 NTHFMLVSEMPHGGQKRSGYGKDMSMYGLEDYTVVRHVMFKH 474 Lambda K H 0.319 0.133 0.404 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: 525 Number of extensions: 21 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: 487 Length of database: 474 Length adjustment: 34 Effective length of query: 453 Effective length of database: 440 Effective search space: 199320 Effective search space used: 199320 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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