Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate HSERO_RS04810 HSERO_RS04810 aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__HerbieS:HSERO_RS04810 Length = 504 Score = 324 bits (830), Expect = 5e-93 Identities = 191/478 (39%), Positives = 264/478 (55%), Gaps = 14/478 (2%) Query: 22 AFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGV---WSQL 78 ++INGE A GE + +P GR AS D A A A W L Sbjct: 25 SWINGELV-AGQGEIIQLYNPATGR-----ASLSYRDGGAAAVEAAAVAAQRAQRQWWAL 78 Query: 79 APAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKV 138 + A R L ++R E LA LE + GKPI D + ++ A+ + A DK Sbjct: 79 SHAARGRALYAVGAVIRAEAEPLARLEAISSGKPIRDCRA-EMQKVAEMFEYYAGWADKF 137 Query: 139 YDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPL 198 Y EV P P L REP G V + PWN P W+LGPALATGN+V+LKPSE +P Sbjct: 138 YGEVIPVPSSHLNYTRREPYGTVLQMTPWNAPAFTCGWQLGPALATGNAVLLKPSELTPF 197 Query: 199 TAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGE 258 +++ IA+L +AG+PAG++NVL G G T+ V ++F GS L+ A Sbjct: 198 SSLAIARLGEQAGLPAGLVNVLAGLGQTMVPQAMATWTVKKVIFVGSPATGA-LIAKAAA 256 Query: 259 SNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKF 318 + + LE GGKS NI+F DA DL+ AA A +AI G+ C AGSRLLV+R + D+F Sbjct: 257 ARVMPCVLELGGKSANIIFEDA-DLRLAAFGAQAAIFSGAGQSCVAGSRLLVQRKVYDRF 315 Query: 319 LPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEET 378 + V + + G PLD T VG + + +Q + + G + GA L AG R EE Sbjct: 316 VETVAAGAEKIRLGAPLDDSTEVGPINNRKQYEHIQRMVARGLEAGATLAAGHTRYGEE- 374 Query: 379 GGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDI 438 G +V PT+ +NAM +A+ EIFGPV I F+ EEA+AIAND+ +GLA +WT D+ Sbjct: 375 -GYFVRPTLLAHASNAMEVARSEIFGPVAVAIPFEDEEEAIAIANDSEFGLAGAVWTRDV 433 Query: 439 SKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIK 496 ++AH+ A +V AG+ WVN Y ++ +PFGGF +SG GR + AL YT+ K+ W++ Sbjct: 434 ARAHRVAASVNAGTFWVNSYKTINVASPFGGFNRSGYGRSSGMEALYDYTQTKSVWVE 491 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: 618 Number of extensions: 26 Number of successful extensions: 4 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: 504 Length adjustment: 34 Effective length of query: 463 Effective length of database: 470 Effective search space: 217610 Effective search space used: 217610 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