Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_010532194.1 ON01_RS16870 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-11560 (497 letters) >NCBI__GCF_000224785.1:WP_010532194.1 Length = 474 Score = 287 bits (735), Expect = 5e-82 Identities = 179/471 (38%), Positives = 263/471 (55%), Gaps = 11/471 (2%) Query: 23 FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82 +INGE+ ++ ET E ++P + ++ D +RAV AR F S +SQ + Sbjct: 8 YINGEWVESTGSETMEVINPATEEVMGHISLGTQEDLDRAVRAARDAFPS--FSQTSKEY 65 Query: 83 RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142 R L + AD K ++L + T ++G P+ S + AE + Sbjct: 66 RIELLEKIADEYEKRKDDLIKVITEELGAPLNLSEKVHYMMGYSHFKQAAEELR----HF 121 Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202 + T + +E +GV G I PWNFP K+ A A G++V+LKP+E +P A+ Sbjct: 122 SFTEKRDKSTIVKEAIGVSGLITPWNFPTNQTSTKIASAFAAGSTVILKPAEITPYAAMI 181 Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262 +A + AG+P GV N++ G G VG A++ H D+D + +TGS +++M A + ++K Sbjct: 182 LADIFEAAGLPKGVFNLVNGTGEGVGNAISSHPDIDFVSYTGSGVAGRKVMENAAK-DIK 240 Query: 263 RIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMV 322 ++ LE GGKSP IV DA D+Q AA+ A + I+ N G+VCTA +R+LV ++IK +F V Sbjct: 241 KVALELGGKSPMIVLEDA-DVQKAAKIAVANISNNTGQVCTAATRVLVPKTIKPQFEEEV 299 Query: 323 VEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEE-TGGT 381 A++ G+P + VG LV +Q + V YI+ G +GAK+L GG E G Sbjct: 300 KAAVEKLTVGDP-EQDNKVGPLVAEKQWDRVQGYIQTGMDEGAKVLIGGVGKPEGLKQGY 358 Query: 382 YVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKA 441 + PT+F V+N M IAQEEIFGPV ++I +DT +EA+ IANDT YGLA + D Sbjct: 359 FAMPTVFTDVSNDMTIAQEEIFGPVTTIIPYDTLDEAIEIANDTIYGLAGYVVGEDPDTL 418 Query: 442 HKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKA 492 K A +RAG + VN D +APFGGFKQSG GR+ +E+Y E KA Sbjct: 419 QKAASGIRAGQIRVNSAP-TDFSAPFGGFKQSGIGREWGDFGIEEYLEPKA 468 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: 506 Number of extensions: 26 Number of successful extensions: 7 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: 474 Length adjustment: 34 Effective length of query: 463 Effective length of database: 440 Effective search space: 203720 Effective search space used: 203720 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