Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_008507152.1 BIBO1_RS11605 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >NCBI__GCF_000182725.1:WP_008507152.1 Length = 483 Score = 319 bits (818), Expect = 1e-91 Identities = 185/475 (38%), Positives = 274/475 (57%), Gaps = 10/475 (2%) Query: 18 IEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQ 77 ++ + +NG + DA G T + +P DG + V S +A A++ A A SG W+ Sbjct: 10 LKSQCLVNGRWIDAADGTTIKVTNPADGSVIGTVPSLSVATIKEAID-ASAKALSG-WAA 67 Query: 78 LAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDK 137 +R L ++ DL+ N +++AL+ T + GKP+ ++ ++ AA I W AE + Sbjct: 68 KTAKERAGILRKWFDLIIANADDIALIMTSEQGKPLAEARG-EVLYAASFIEWFAEEAKR 126 Query: 138 VYDEVAPTPHDQLGL-VTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKS 196 VY + P P + L V R+PVGV AI PWNFP M K PALA G +++++P++ + Sbjct: 127 VYGDTIPAPQNGQRLTVIRQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMIVRPADLT 186 Query: 197 PLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYA 256 PLTA+ + LA +AGIPAGVL ++ G +G L + V L FTGST++ + LM Sbjct: 187 PLTALALGVLAEKAGIPAGVLQIVTGKAREIGAELTSNDTVRKLSFTGSTEVGRLLMAQC 246 Query: 257 GESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKD 316 + +KRI LE GG +P IVF DA DL AA + A + N G+ C +R+ V+R + D Sbjct: 247 APT-IKRISLELGGNAPFIVFDDA-DLDAAVDGAMVSKYRNAGQTCVCANRIYVQRGVYD 304 Query: 317 KFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLE 376 KF + +K K GN +P +G +++ + + V ++IE GAKL+AGGK Sbjct: 305 KFAEKLAAKVKELKVGNGTEPGVVIGPMIEEKAITKVKAHIEDAVSKGAKLIAGGK---- 360 Query: 377 ETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTS 436 E GG + EP I GVT+ M +A+EE FGP+ + AFDT EE +A ANDT +GLAA +T Sbjct: 361 ELGGLFFEPGILTGVTSDMLVAKEETFGPLAPLFAFDTEEEVIAQANDTIFGLAAYFYTE 420 Query: 437 DISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491 + S+A + + A+ G V N + APFGG KQSG GR+ S + +E+Y E K Sbjct: 421 NFSRAIRVSEALEYGMVGHNTGLISNEVAPFGGVKQSGLGREGSKYGIEEYLETK 475 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: 573 Number of extensions: 39 Number of successful extensions: 6 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: 483 Length adjustment: 34 Effective length of query: 463 Effective length of database: 449 Effective search space: 207887 Effective search space used: 207887 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