Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_023433101.1 N177_RS14415 aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >NCBI__GCF_000496075.1:WP_023433101.1 Length = 492 Score = 335 bits (860), Expect = 2e-96 Identities = 196/480 (40%), Positives = 276/480 (57%), Gaps = 9/480 (1%) Query: 21 RAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAP 80 R +I+G + + +G +FE + P G A + + + AD +RAV A F+ WS+L Sbjct: 7 RNYIDGAFCEGGAG-SFESVDPATGEAWANMPAANAADVDRAVRAADRAFHDPSWSRLTA 65 Query: 81 AKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYD 140 +R L R ADL+ +N + LA LET D GK I ++S+ I A + A DK+ Sbjct: 66 TQRGKLLYRLADLVAENAQALAELETRDTGKIIRETSA-QIAYVADYYRYYAGLADKI-- 122 Query: 141 EVAPTPHDQLGLVT---REPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSP 197 E A P D+ + T REP+GVV A+VPWN L ++ KLGPALA G +VVLK SE P Sbjct: 123 EGAHLPIDKPDMETYLRREPIGVVAAVVPWNSQLFLSAVKLGPALAAGCTVVLKASEDGP 182 Query: 198 LTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAG 257 + A+L +AG P GV+N+L G+G G ALA H V + FTG A+ ++ ++ Sbjct: 183 APLLAFARLVDQAGFPPGVVNILTGFGDQCGSALASHPLVARIAFTGGPATARHIVRHSA 242 Query: 258 ESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDK 317 E N+ + LE GGKSP +VF DA DL + A A + I G+ C AGSRL+V+R IKD Sbjct: 243 E-NLAAVTLELGGKSPVVVFEDA-DLDSVANAVVAGIFAATGQSCVAGSRLIVQRGIKDA 300 Query: 318 FLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEE 377 L +V+ + + G+P +T +G L +Q+ + I G +L+ GG R Sbjct: 301 LLERLVQKARAIRIGDPQAQETEMGPLATARQLRHIEDVIARSLAAGGRLVTGGGRPDGF 360 Query: 378 TGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSD 437 G Y EPTI D + +EE+FGPVLSV+ F+ EAV AN TPYGLA+G++T+ Sbjct: 361 PAGHYFEPTIIDCDATTIPSVEEELFGPVLSVLGFEEETEAVEFANRTPYGLASGVFTAS 420 Query: 438 ISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIKL 497 +++AH+ RA+RAG VWVN Y PFGG+ SG+GR+ L A YT KA WI++ Sbjct: 421 LTRAHRMIRAIRAGVVWVNTYRAVSPIMPFGGYGLSGSGREGGLDAALDYTRTKAVWIRV 480 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: 634 Number of extensions: 25 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: 492 Length adjustment: 34 Effective length of query: 463 Effective length of database: 458 Effective search space: 212054 Effective search space used: 212054 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 24 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