Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_004687625.1 BMI_RS15595 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase
Query= reanno::WCS417:GFF5420 (497 letters) >NCBI__GCF_000022745.1:WP_004687625.1 Length = 504 Score = 362 bits (930), Expect = e-104 Identities = 205/468 (43%), Positives = 275/468 (58%), Gaps = 5/468 (1%) Query: 24 INGEYTAAVSGDTFECISPVDGRLLATVASCDAADAQRAVENARATFNSGVWSRLAPAKR 83 I GE AA G TFE ISPVD + LATVA AAD RA A+A F W+ ++ R Sbjct: 26 IGGEDVAAADGATFETISPVDLKPLATVALGKAADIDRAARAAKAAFPE--WAAMSGDAR 83 Query: 84 KSAMLRFAALLKANAEELALLETLDMGKPISDSLNIDVPGAANALSWSGEAIDKIYDEVA 143 K + + A + A AEE+A +E +D G+ + + GA N ++ A + + Sbjct: 84 KKLLHKIADAIVARAEEIAFVECMDTGQSLKFMAKAALRGAENFRFFADRAPEARDGKTL 143 Query: 144 ATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEKSPLTAIRI 203 P Q+ + TR P+G VG I PWN P M++ WK+ PAL+ G +V+ KP+E SPLTA + Sbjct: 144 RGP-GQVNMTTRVPIGPVGVITPWNTPFMLSTWKIAPALAAGCTVVHKPAEFSPLTARLL 202 Query: 204 AALAVEAGIPKGVFNVLPGYGHTVGNALALHMDVDTLVFTGSTKIAKQLLIRSGESNMKR 263 +A EAG+PKGV+N++ G+G G AL H D+ + F G ++ L+++ G +KR Sbjct: 203 VEIAEEAGLPKGVWNLVNGFGEDAGKALTEHPDIKAIGFVGESRTGS-LIMKQGADTLKR 261 Query: 264 VWLEAGGKSPNIVFADAPDLQAAAESAAGAIAFNQGEVCTAGSRLLVERSIKDKFLPLVI 323 V E GGK+P +VFADA DL+ A ++A I GE CT+ SRLLVE SI +KF LV Sbjct: 262 VHFELGGKNPVVVFADA-DLERAVDAAVFMIYSLNGERCTSSSRLLVEASIYEKFTALVA 320 Query: 324 EALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHADGAKLVAGGKRTLEETGGTYV 383 E K K G+PLDP T VG L+ VL YIE G ++GA + AGG + GG YV Sbjct: 321 EKAKRIKVGHPLDPETVVGPLIHPVHEKKVLEYIEIGRSEGATVAAGGAKFAGPGGGCYV 380 Query: 384 EPTIFDGVTNAMKIAKEEIFGPVLSVITFDSAEEAVAIANDTIYGLAAAVWTADISKAHL 443 PT+F N M+IA+EEIFGPVL+ I F EA+A+AND YGL +WT D+++A Sbjct: 381 SPTLFTAAHNGMRIAQEEIFGPVLTAIPFKDEAEALALANDVKYGLTGYLWTNDVTRAFR 440 Query: 444 TAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELK 491 AL AG +WVN + + PFGG K SG GRD +FD Y E K Sbjct: 441 FTDALEAGMIWVNSENVRHLPTPFGGVKNSGIGRDGGDWSFDFYMETK 488 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: 656 Number of extensions: 32 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: 504 Length adjustment: 34 Effective length of query: 463 Effective length of database: 470 Effective search space: 217610 Effective search space used: 217610 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