Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate GFF657 Psest_0671 NAD-dependent aldehyde dehydrogenases
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__psRCH2:GFF657 Length = 506 Score = 353 bits (905), Expect = e-101 Identities = 205/483 (42%), Positives = 282/483 (58%), Gaps = 12/483 (2%) Query: 16 LKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVW 75 LK FINGE+ + V+G+ F LSPV+G+ +A+ D AD +A++ A A ++ W Sbjct: 15 LKARYGNFINGEFVEPVNGQYFTNLSPVNGQPIAEFPRSDAADIEKALDAAHAAADA--W 72 Query: 76 SQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAI 135 + + R L++ AD + +N+E LA+ ET D GK + ++ + DIP AA + A I Sbjct: 73 GKTSVQARSLILLQIADRIEQNLEMLAVTETWDNGKAVRETLNADIPLAADHFRYFAGCI 132 Query: 136 DKVYDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEK 195 A EP+GVVG I+PWNFP+LMA WKL PALA GN VVLKP+E+ Sbjct: 133 RAQEGTSAEIDEHTAAYHFHEPLGVVGQIIPWNFPILMAAWKLAPALAAGNCVVLKPAEQ 192 Query: 196 SPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVY 255 +PL I + I +P GVLNV+ GYG G+ALA + + FTGST + +M Sbjct: 193 TPL-GITVLMEVIGDLLPPGVLNVVQGYGREAGEALASSKRIAKIAFTGSTPVGSHIMKR 251 Query: 256 AGESNMKRIWLEAGGKSPNIVFADAPDLQAA-AEAAASAIA---FNQGEVCTAGSRLLVE 311 A E+ + +E GGKSPNI F D + E AA + FNQGEVCT SR LV+ Sbjct: 252 AAEAIIPST-VELGGKSPNIYFEDIMQAEPTFIEKAAEGLVLGFFNQGEVCTCPSRALVQ 310 Query: 312 RSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGG 371 SI F+ V++ + K G+PLD +T VGA QQ + ++SY+E +GA++L GG Sbjct: 311 ESIYAPFMEAVMKKVAQIKRGDPLDTETMVGAQASQQQFDKIMSYLEIAKGEGAEVLTGG 370 Query: 372 KRTLEETG---GTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYG 428 E G Y++PT+ G TN MR+ QEEIFGPV+ V F EA+AIANDT YG Sbjct: 371 AAEKLEGSLATGYYIQPTLLKG-TNQMRVFQEEIFGPVIGVTTFKDEAEALAIANDTEYG 429 Query: 429 LAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYT 488 L AG+WT DI++A++ RA++AG VW N Y A FGG+K+SG GR+ L+ Y Sbjct: 430 LGAGVWTRDINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKRSGVGRETHKMILDSYQ 489 Query: 489 ELK 491 + K Sbjct: 490 QTK 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: 628 Number of extensions: 41 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