Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 202599 SO3496 aldehyde dehydrogenase (NCBI ptt file)
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__MR1:202599 Length = 498 Score = 760 bits (1963), Expect = 0.0 Identities = 364/496 (73%), Positives = 425/496 (85%) Query: 2 TTLTRADWEQRAQQLKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANR 61 T TR+DWE A L I G+AFINGEY DA SG TF+C+SP+DGR LA VASCDL DAN Sbjct: 3 TPKTRSDWENLAVSLAINGKAFINGEYRDASSGNTFDCISPIDGRLLAPVASCDLMDANI 62 Query: 62 AVENARATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDI 121 AV NAR F+SGVWS+ AP KRK +IRFA+LL +N ELALLETLDMGKPI S ++D+ Sbjct: 63 AVANAREVFDSGVWSKAAPVKRKQVMIRFAELLEENANELALLETLDMGKPIRFSKAVDV 122 Query: 122 PGAAQAIHWTAEAIDKVYDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPA 181 GAA+AI W+ EAIDK+YDE+APT H+++G++TREPVGVV AIVPWNFPLLMACWKLGPA Sbjct: 123 AGAARAIRWSGEAIDKLYDELAPTAHNEIGMITREPVGVVAAIVPWNFPLLMACWKLGPA 182 Query: 182 LATGNSVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLV 241 L TGNSV+LKPSEKSPLTAIRIA+LA++AGIP GVLNVLPGYGHTVGKALALHMDVDTLV Sbjct: 183 LVTGNSVILKPSEKSPLTAIRIAELAVQAGIPKGVLNVLPGYGHTVGKALALHMDVDTLV 242 Query: 242 FTGSTKIAKQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEV 301 FTGSTKIAKQLM+YAGESNMKR+WLEAGGKSPNIVF DAPDL+AAA AAA AI FNQGEV Sbjct: 243 FTGSTKIAKQLMIYAGESNMKRVWLEAGGKSPNIVFNDAPDLKAAAVAAAEAIGFNQGEV 302 Query: 302 CTAGSRLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGH 361 CTAGSRLLVE +KD+ + ++ E L W+PG+PL+P T GA+VD QQ++T+LSYI+AG Sbjct: 303 CTAGSRLLVESGVKDELVGLIAEELASWQPGHPLEPTTVSGAVVDKQQLDTILSYIKAGQ 362 Query: 362 KDGAKLLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAI 421 +GA L+ GG++ L ETGG YV+PT+F V N M+IA EEIFGPVLSVI F+ EEA+AI Sbjct: 363 NEGASLVYGGQQVLAETGGVYVQPTVFSNVKNQMKIASEEIFGPVLSVIEFNGMEEAIAI 422 Query: 422 ANDTPYGLAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSL 481 ANDT YGLAAG+WT+DISKAHKTA+A+R+G VW+N YDGGDMTAPFGG+KQSGNGRDKSL Sbjct: 423 ANDTIYGLAAGVWTADISKAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSL 482 Query: 482 HALEKYTELKATWIKL 497 H+ +KYTE+KATWI L Sbjct: 483 HSFDKYTEIKATWIVL 498 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: 849 Number of extensions: 33 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: 498 Length adjustment: 34 Effective length of query: 463 Effective length of database: 464 Effective search space: 214832 Effective search space used: 214832 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 Apr 09 2024. 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