Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_035239838.1 Q366_RS13505 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >NCBI__GCF_000745975.1:WP_035239838.1 Length = 484 Score = 315 bits (807), Expect = 2e-90 Identities = 186/470 (39%), Positives = 266/470 (56%), Gaps = 8/470 (1%) Query: 23 FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82 FI E+ A SG+T + +P G+ L V C + RA+ A + ++ W + Sbjct: 15 FIQDEWVAADSGKTVDVTNPATGQILGTVPFCGADETQRAINAANESLDA--WRSKTAGE 72 Query: 83 RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142 R A L ++ DLL +N E+LA++ T + GKP+ +S +I AA W AE +VY +V Sbjct: 73 RSAILRKWYDLLMENQEDLAVIMTAEQGKPLAESRG-EIAYAAAFFEWFAEEAKRVYGDV 131 Query: 143 AP-TPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAI 201 P T Q +V ++PVGVV AI PWNFP M K G ALA G ++VLKP+ +P +A+ Sbjct: 132 IPQTVASQRLVVIKQPVGVVAAITPWNFPSAMITRKAGAALAAGCTMVLKPATATPFSAL 191 Query: 202 RIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNM 261 IA+L +AG+P GV NV+ G +G L + V L FTGST++ K+LM M Sbjct: 192 AIAKLGQQAGVPKGVFNVVTGSSSAIGGELTANPIVRKLTFTGSTQVGKKLMRDCA-GTM 250 Query: 262 KRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPM 321 KR+ +E GG +P IVF DA D+ AA E A + N G+ C +R+ V+ + D+F Sbjct: 251 KRLSMELGGNAPFIVFDDA-DIDAAVEGAMACKYRNSGQTCVCANRMYVQAGVYDEFCRK 309 Query: 322 VVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGT 381 + A++ K GN D G L+D + TV S+I+ G K+LAGG R G T Sbjct: 310 LTAAVQELKVGNGFDDGVQQGPLIDMAAVETVESHIKDAVDKGGKVLAGGTR--HALGRT 367 Query: 382 YVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKA 441 + PTI VT+ MR+A+EE FGP+ V FDT EE V ANDT +GLAA +T D++++ Sbjct: 368 FFAPTIIADVTDDMRVAREETFGPLAPVFKFDTEEEVVRKANDTEFGLAAYFYTRDMARS 427 Query: 442 HKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491 + + G V +N + APFGG K+SGNGR+ S + L+ Y E+K Sbjct: 428 WRIGEKLEYGLVGINSGIISNPVAPFGGVKESGNGREGSKYGLDDYLEIK 477 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: 576 Number of extensions: 31 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: 484 Length adjustment: 34 Effective length of query: 463 Effective length of database: 450 Effective search space: 208350 Effective search space used: 208350 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 Apr 09 2024. 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