Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_011318370.1 AVA_RS07875 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-11560 (497 letters) >NCBI__GCF_000204075.1:WP_011318370.1 Length = 498 Score = 302 bits (774), Expect = 2e-86 Identities = 173/482 (35%), Positives = 274/482 (56%), Gaps = 17/482 (3%) Query: 23 FINGEYTDAVSGETFECLSPVD-GRFLAKVASCDLADANRAVENARATFNSGVWSQLAPA 81 +ING++ +A + T +P + +A D +RAV AR + S W ++ Sbjct: 10 YINGQWLNAATETTLNSHNPANKSEIVATFPRSQADDTDRAVTAARQAYGS--WRKVPAP 67 Query: 82 KRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDE 141 R + R +LL ++ EELA L + +MGKPI ++ D+ ++A +++ + Sbjct: 68 ARAEYIFRVGELLLQHKEELAQLISREMGKPITEARG-DVQEGVDCAFYSAGEGRRLFGQ 126 Query: 142 VAPTPH-DQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTA 200 P+ ++ + R P+GV I PWNFP+ + CWK PAL GN+V+LKP+E +P A Sbjct: 127 TTPSEMPNKFAMTVRMPIGVCALITPWNFPVAIPCWKAMPALVCGNTVILKPAEDTPACA 186 Query: 201 IRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGES- 259 ++ ++ AG+P GV+N++ G G GKAL H ++D + FTGS+ Y GE+ Sbjct: 187 TKLIEIFAAAGLPPGVINLVHGVGEEAGKALVEHPNIDLVSFTGSSATG----AYVGETC 242 Query: 260 --NMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDK 317 KR+ LE GGK+ +V DA DL+ A + A G+ CTA SRL++ R IK+K Sbjct: 243 GRTHKRVCLEMGGKNAQVVMEDA-DLELALDGALWGAFGTTGQRCTATSRLILHRDIKEK 301 Query: 318 FLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEE 377 F M+ E + G +P+T +G +++ +Q+ V Y+ ++GAK+L GG+ E Sbjct: 302 FTTMLRERTSQLRLGAGTEPETDIGPIINNRQLQRVHEYMNIAREEGAKILIGGEIVTEG 361 Query: 378 --TGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWT 435 G + +PTI D VT MR+A+EEIFGPV+++I T EEA+AI NDT YGL++ ++T Sbjct: 362 QLKQGYFFQPTILDNVTPQMRVAREEIFGPVVALIEVSTFEEAIAILNDTKYGLSSSVYT 421 Query: 436 SDISKAHKTARAVRAGSVWVN-QYDGGDMTAPFGGFKQSGNG-RDKSLHALEKYTELKAT 493 DI++A R + G ++N G ++ PFGG KQ+GNG R+ AL+ +TE K+ Sbjct: 422 RDINRAFVAMRDIEVGITYINGPTIGAEVHLPFGGVKQTGNGHREAGTTALDVFTEWKSV 481 Query: 494 WI 495 ++ Sbjct: 482 YV 483 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: 595 Number of extensions: 24 Number of successful extensions: 6 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