Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_085772038.1 B1812_RS13395 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-11560 (497 letters) >NCBI__GCF_002117405.1:WP_085772038.1 Length = 506 Score = 376 bits (966), Expect = e-109 Identities = 211/477 (44%), Positives = 293/477 (61%), Gaps = 14/477 (2%) Query: 23 FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82 FI G++ + GE F+ +SP+ G + +VA AD A++ A ++ W + A+ Sbjct: 22 FIGGQWVAPLGGEYFDNISPITGHPICQVARGRAADVELALDAAHKAKDA--WGKTPAAE 79 Query: 83 RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142 R L + A L N+ LAL+ET+D GKPI ++++ DIP A + A + + Sbjct: 80 RANMLNKIAQRLDDNLSALALVETIDNGKPIRETTAADIPLAIDHFRYFAGCLRAQEGSL 139 Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202 + HD + EP+GVVG I+PWNFP+LMA WKL PALA GN VVLKP+E++P++ + Sbjct: 140 SEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAAWKLSPALAAGNCVVLKPAEQTPMSILA 199 Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262 +A+L + +P GVLN++ G+G GK LA + + + FTG T + +M YA E N+ Sbjct: 200 VAELIADL-LPPGVLNIVNGFGVEAGKPLASNKRIAKIAFTGETTTGRLIMQYAAE-NLI 257 Query: 263 RIWLEAGGKSPNIVFAD--APD---LQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDK 317 + LE GGKSPNI FAD A D L A E AS A NQGEVCT SR LV+RSI DK Sbjct: 258 PVTLELGGKSPNIFFADVMAEDDAFLDKALEGFAS-FALNQGEVCTCPSRALVQRSIYDK 316 Query: 318 FLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTL-- 375 F+ + + + G+PLDP T +GA Q+ +LSY++ G K+GAK+L GG+R++ Sbjct: 317 FMEKALARVAKIRQGHPLDPATMIGAQASNDQLEKILSYVDIGRKEGAKVLIGGERSVLE 376 Query: 376 -EETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIW 434 E G Y++PT +G N MR+ QEEIFGPV+SV F+T EEA+ IANDT YGL AG+W Sbjct: 377 GELKEGYYMQPTALEG-HNRMRVFQEEIFGPVVSVTTFETEEEALQIANDTLYGLGAGLW 435 Query: 435 TSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491 T D S+A++ RA+RAG VW N Y A FGG+KQSG GR+ L+ Y + K Sbjct: 436 TRDGSRAYRCGRAIRAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHKMMLDHYQQTK 492 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: 627 Number of extensions: 29 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: 506 Length adjustment: 34 Effective length of query: 463 Effective length of database: 472 Effective search space: 218536 Effective search space used: 218536 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