Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate H281DRAFT_02299 H281DRAFT_02299 aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__Burk376:H281DRAFT_02299 Length = 506 Score = 352 bits (902), Expect = e-101 Identities = 196/476 (41%), Positives = 278/476 (58%), Gaps = 12/476 (2%) Query: 23 FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82 FI GE+ GE F+ +SP+ G + AD A++ A W + + Sbjct: 22 FIGGEWVKPAGGEYFDNVSPITGEPFTSIPRSREADVELALDAAHRA--KAAWGKTSTTD 79 Query: 83 RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142 R L R AD + N++ LA+ ET+D GKP+ ++ + DIP A + A A+ + Sbjct: 80 RANILNRIADRMEANLQRLAVAETIDNGKPLRETMAADIPLAIDHFRYFAGAVRAQEGSI 139 Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202 + D + EP+GVVG I+PWNFP+LMA WKL PALA GN VVLKP+E++P + + Sbjct: 140 SEIDDDTVAYHFHEPLGVVGQIIPWNFPILMAVWKLAPALAAGNCVVLKPAEQTPASILV 199 Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262 + +L I+ +PAGVLNV+ G+G GK LA + + FTG T + +M YA + N+ Sbjct: 200 LVEL-IQDLLPAGVLNVVNGFGLEAGKPLASSKRIAKIAFTGETTTGRLIMQYASQ-NII 257 Query: 263 RIWLEAGGKSPNIVFADAPDLQAA----AEAAASAIAFNQGEVCTAGSRLLVERSIKDKF 318 + LE GGKSPNI FAD + + A + A NQGEVCT SR+L++ I D F Sbjct: 258 PVTLELGGKSPNIFFADVMNQDDSYFDKALEGFAMFALNQGEVCTCPSRVLIDEKIYDSF 317 Query: 319 LPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTL--- 375 + ++ + G+PLD +T +GA +Q+ +LSY++ G ++GA+ L GG+R Sbjct: 318 MERALKRVAAITQGHPLDTRTMIGAQASQEQLEKILSYVDLGKQEGAECLIGGERNTLSG 377 Query: 376 EETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWT 435 E + G YV+PT+F G N MRI QEEIFGPV+SV F T EEA+ IANDT YGL AG+WT Sbjct: 378 ELSKGYYVKPTVFRG-HNKMRIFQEEIFGPVVSVTTFKTEEEALEIANDTLYGLGAGVWT 436 Query: 436 SDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491 D ++A++ R ++AG VW N Y A FGG+KQSG GR+ L+ Y + K Sbjct: 437 RDGTRAYRFGRQIQAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHKMMLDHYQQTK 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: 641 Number of extensions: 38 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: 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 Sep 17 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