Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_058929223.1 AU252_RS01555 aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >NCBI__GCF_001484605.1:WP_058929223.1 Length = 508 Score = 391 bits (1004), Expect = e-113 Identities = 210/478 (43%), Positives = 293/478 (61%), Gaps = 7/478 (1%) Query: 24 INGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAKR 83 I+G + + SGETF C+ P D +V + + D +RAV AR F+ G W Q P++R Sbjct: 25 IDGAWVQSSSGETFACVDPYDNASWGRVPAATVEDVDRAVRAARRAFDEGGWPQTLPSQR 84 Query: 84 KAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEVA 143 A L RFADLL +N +ELA + + GK IG+ + + Q H+ A + + Sbjct: 85 AALLRRFADLLTENADELARGQIHENGKLIGEMTWGALQ-MGQHAHYVAGLAETIQGRTI 143 Query: 144 PTPHDQLGLVT-REPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202 + T REP+GVV I PWN PL++ WKL ALA GN+VV+KPSE +P + +R Sbjct: 144 ESNWPNTAAFTFREPIGVVAMITPWNSPLMLLSWKLFAALAAGNTVVIKPSEATPTSTLR 203 Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262 +A+LA+EAG P GV+NV+ G+G G AL H VD + FTGST + + A E Sbjct: 204 MAELAMEAGFPPGVINVVTGFGQPTGSALVDHRGVDKIAFTGSTSAGRAINKQAAE-RFA 262 Query: 263 RIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMV 322 R+ LE GGKSPNI+F+DA D+ A A + I G+ C GSR+LV+ SI D F+ + Sbjct: 263 RVTLELGGKSPNIIFSDA-DIDNAVHGAMAGIFGATGQTCMGGSRVLVQDSIYDDFVDRM 321 Query: 323 VEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKR---TLEETG 379 A + G+PLDP +G + + Q V+ Y++ G +GA+++AGG R T E + Sbjct: 322 ARATQALTLGDPLDPTVDMGPVSNRAQFQKVIDYVDLGQSEGAEVVAGGARCMTTSELSK 381 Query: 380 GTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDIS 439 G + EPT+F V+N R+AQEEIFGPV S+I F +EAV IAN + +GLAAG+WT+D+S Sbjct: 382 GLFFEPTVFANVSNESRLAQEEIFGPVASIIRFRDEDEAVKIANASDFGLAAGVWTNDVS 441 Query: 440 KAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIKL 497 +AH+ R VR+G+VWVN Y + + PFGGFKQSG GR+ AL+ YTE+K+ WI L Sbjct: 442 RAHRMIRRVRSGTVWVNTYRLTNYSVPFGGFKQSGIGRELGPDALDAYTEVKSAWIDL 499 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: 609 Number of extensions: 27 Number of successful extensions: 5 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: 508 Length adjustment: 34 Effective length of query: 463 Effective length of database: 474 Effective search space: 219462 Effective search space used: 219462 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