Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_011383257.1 AMB_RS04160 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >NCBI__GCF_000009985.1:WP_011383257.1 Length = 499 Score = 277 bits (708), Expect = 7e-79 Identities = 165/476 (34%), Positives = 259/476 (54%), Gaps = 9/476 (1%) Query: 18 IEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQ 77 I+ A+++G + A G F+ L P G +A V + RA++ A A +N W Q Sbjct: 23 IKSHAYVDGVWVGADDGRRFDVLDPATGGLIASVPDLGATETRRAIDAAEAAWNP--WRQ 80 Query: 78 LAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDK 137 R A ++ + DL+ + + LA L + + GKP+ ++ +I A I W AE + Sbjct: 81 RTAKDRAAVMMAWHDLIMAHQDALARLLSAEQGKPLAEAMG-EISYGASFISWFAEEGKR 139 Query: 138 VYDEVAPTP-HDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKS 196 Y ++ PT D+ LV ++P+GVV A+ PWNFP+ M K PALA G VV+KP+E + Sbjct: 140 AYGDLIPTTASDRRLLVMKQPIGVVAAVTPWNFPMAMITRKCAPALAAGCPVVVKPAEDT 199 Query: 197 PLTAIRIAQLAIEAGIPAGVLNVL-PGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVY 255 PL+A+ +A+LA AG+P G+ N++ VG + + V L FTGST++ K LM Sbjct: 200 PLSALALAELAHRAGLPKGLFNIVTTRQPAAVGGEMTGNAKVRKLSFTGSTRVGKLLMAQ 259 Query: 256 AGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIK 315 E+ +K++ LE GG +P IVF D DL AA A ++ N G+ C +R LV+ I Sbjct: 260 CAET-VKKVSLELGGNAPFIVFDDC-DLDAAVAGALASKYRNSGQTCICTNRFLVQAGIY 317 Query: 316 DKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTL 375 + F + E G+ L G L++ + V +++ GA++L GG+ Sbjct: 318 EDFAVKLAEKAAAMAVGHALSGVVQQGPLINAAAVAKVAAHVADAVSKGARVLTGGRP-- 375 Query: 376 EETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWT 435 GG + +PT+ VT AM +EE FGPV ++ F+T EA+A+AN + +GLA ++ Sbjct: 376 HALGGGFWQPTVLADVTPAMLCFREETFGPVAPLLRFETEAEAIALANASEFGLAGYFYS 435 Query: 436 SDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491 D+++ + A A+ G V VN+ + APFGG K+SG GR+ S + L+ + E K Sbjct: 436 RDVARVFRVAEALECGMVGVNESLISNEVAPFGGIKESGLGREGSKYGLDDFMETK 491 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: 579 Number of extensions: 24 Number of successful extensions: 7 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: 499 Length adjustment: 34 Effective length of query: 463 Effective length of database: 465 Effective search space: 215295 Effective search space used: 215295 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