Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_090442712.1 BLS63_RS08515 aldehyde dehydrogenase
Query= reanno::WCS417:GFF5420 (497 letters) >NCBI__GCF_900100495.1:WP_090442712.1 Length = 497 Score = 565 bits (1457), Expect = e-165 Identities = 270/494 (54%), Positives = 362/494 (73%) Query: 4 LTRADWEQRAKDLKIEGRAYINGEYTAAVSGDTFECISPVDGRLLATVASCDAADAQRAV 63 L +DW++RA + +A I+G+ A SG TF I+P + +LLA VA+CDAAD AV Sbjct: 2 LQHSDWQRRAAEQGFISQALIDGQLRPAQSGATFASINPANNQLLAEVAACDAADVDAAV 61 Query: 64 ENARATFNSGVWSRLAPAKRKSAMLRFAALLKANAEELALLETLDMGKPISDSLNIDVPG 123 +AR F G W+R+AP +RK +LR A L+ AN EELALL++L+MGKP+ D+ IDVPG Sbjct: 62 ASARQAFEQGPWARMAPRERKQVLLRLAELIMANREELALLDSLNMGKPVMDAYTIDVPG 121 Query: 124 AANALSWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALS 183 AAN +W EA+DK YD++A T D L ++REP+GV+GA+VPWNFPL +A WKL PAL+ Sbjct: 122 AANVFAWYAEALDKRYDQIAPTASDALATISREPLGVIGAVVPWNFPLDLAAWKLSPALA 181 Query: 184 TGNSVILKPSEKSPLTAIRIAALAVEAGIPKGVFNVLPGYGHTVGNALALHMDVDTLVFT 243 GNSV+LKP+E+SP +A+R+ LA+EAG+P GV NVLPG G + G AL LHMDVD L FT Sbjct: 182 AGNSVVLKPAEQSPFSALRLGQLALEAGLPAGVLNVLPGLGESAGKALGLHMDVDCLAFT 241 Query: 244 GSTKIAKQLLIRSGESNMKRVWLEAGGKSPNIVFADAPDLQAAAESAAGAIAFNQGEVCT 303 GST++ K + + +SN+K+VWLE GGKS N+VFAD DL AAE AA AI FNQGEVC+ Sbjct: 242 GSTEVGKCFMAYAAQSNLKQVWLECGGKSANLVFADCQDLDLAAEKAAFAIFFNQGEVCS 301 Query: 304 AGSRLLVERSIKDKFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHAD 363 A SRLLVER + D+F+ +I + W+PG+PL+PA+ GA+VD++Q ++ +I+ Sbjct: 302 ANSRLLVERRVHDEFVQRLIAKAREWQPGDPLNPASRAGAIVDSRQAERIMGFIDRAQGQ 361 Query: 364 GAKLVAGGKRTLEETGGTYVEPTIFDGVTNAMKIAKEEIFGPVLSVITFDSAEEAVAIAN 423 GA LV GG+R +++PT F GV+ AM++A+EE+FGPVL+V+ FDS E+A+A+AN Sbjct: 362 GATLVCGGQRLSVGGSDNFIQPTTFTGVSPAMQLAREEVFGPVLAVLPFDSEEQAIALAN 421 Query: 424 DTIYGLAAAVWTADISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHA 483 D++YGLAA++WT D+++AH A+ LRAGSV VN D D+ PFGG KQSG GRD SLHA Sbjct: 422 DSLYGLAASLWTDDLNRAHRVARRLRAGSVSVNTVDALDVCVPFGGCKQSGFGRDLSLHA 481 Query: 484 FDKYTELKATWIKL 497 FDKY+ LK TW +L Sbjct: 482 FDKYSLLKTTWFQL 495 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: 644 Number of extensions: 29 Number of successful extensions: 2 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: 497 Length adjustment: 34 Effective length of query: 463 Effective length of database: 463 Effective search space: 214369 Effective search space used: 214369 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