Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate H281DRAFT_00993 H281DRAFT_00993 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__Burk376:H281DRAFT_00993 Length = 497 Score = 531 bits (1367), Expect = e-155 Identities = 256/495 (51%), Positives = 351/495 (70%), Gaps = 1/495 (0%) Query: 4 LTRADWEQRAQQLKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAV 63 +T +W+Q+A L ++GRAFI G+ +A S ETF L+P G+ LA +A CD D +RAV Sbjct: 2 MTYQEWKQKADALSLDGRAFIAGQRANAASNETFATLNPSTGKVLADIAKCDTKDVDRAV 61 Query: 64 ENARATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPG 123 AR F SGVWS+ APA+RKA L R A L+ N EELALLE L+ GKPI + +DIP Sbjct: 62 AAAREAFESGVWSKAAPAQRKAVLQRLAQLIDDNAEELALLEALEAGKPISECLGLDIPE 121 Query: 124 AAQAIHWTAEAIDKVYDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALA 183 +A I W AE DK YD ++P+ + ++TREP+GVVGA++PWNFP LM WK+GPAL+ Sbjct: 122 SAACIRWHAEVTDKRYDALSPSGASVVSMITREPIGVVGAVLPWNFPALMLAWKIGPALS 181 Query: 184 TGNSVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFT 243 GNSV++KP+E++ L+ +RIA LA+EAG+PAGVLNV+ G+G + G+AL H DVD + FT Sbjct: 182 VGNSVIVKPAEQTSLSTLRIADLALEAGLPAGVLNVVTGFGESAGQALGRHADVDLVAFT 241 Query: 244 GSTKIAKQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCT 303 GST+ K+ + Y+ ++N+KR+ LE GGK+P +V D +L A AE A +A +N GE C+ Sbjct: 242 GSTETGKRFLRYSADTNLKRVVLECGGKNPQVVLPDVANLDAVAEQAVAAAFWNMGENCS 301 Query: 304 AGSRLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKD 363 AGSR+LV S+K L V+ L+ WK G+PLDP +G+L++ VL++IE + Sbjct: 302 AGSRILVPSSLKASLLEKVLAVLEVWKTGDPLDPDVKLGSLIEEMHFEKVLAHIEKARAE 361 Query: 364 GAKLLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIAN 423 GA+L+ GGK T ++GG +VEPTIFD VT MRIA++E+FGPV+ I + +EAV IAN Sbjct: 362 GARLVCGGKATRTDSGGWFVEPTIFDNVTPQMRIARDEVFGPVVCFIEYADIDEAVHIAN 421 Query: 424 DTPYGLAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSG-NGRDKSLH 482 DT YGLAA +WT +++ AHK A +RAG+V VN + GD++ PFGGFKQSG GRDKS++ Sbjct: 422 DTCYGLAASLWTDNVNHAHKIAARIRAGTVTVNCFGEGDLSTPFGGFKQSGFGGRDKSVY 481 Query: 483 ALEKYTELKATWIKL 497 A ++Y ELK TW+KL Sbjct: 482 AHDQYCELKTTWLKL 496 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: 663 Number of extensions: 24 Number of successful extensions: 2 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: 497 Length adjustment: 34 Effective length of query: 463 Effective length of database: 463 Effective search space: 214369 Effective search space used: 214369 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