Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_011383730.1 AMB_RS06710 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >NCBI__GCF_000009985.1:WP_011383730.1 Length = 485 Score = 297 bits (760), Expect = 6e-85 Identities = 182/477 (38%), Positives = 265/477 (55%), Gaps = 11/477 (2%) Query: 18 IEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQ 77 + A+ING + A SGE +P DG + +V + A+ +A+E A + G W Sbjct: 10 LRDHAYINGSWVAAQSGERLAVTNPADGSLIIRVPAMGAAETRQAIEAADRAW--GPWKA 67 Query: 78 LAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDK 137 +R A L R+ +L+ +LA L T + GKP+ ++ ++ A + W AE + Sbjct: 68 KTAKERSAVLRRWFELIMAAQNDLAKLMTAEQGKPLAEAKG-EVAYGASFVEWFAEEAKR 126 Query: 138 VYDEVAPT--PHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEK 195 VY + P P ++ +V +EP+GVV AI PWNFPL M K PALA G VV+KP+E Sbjct: 127 VYGDTIPEHMPGRRI-VVVKEPIGVVAAITPWNFPLAMITRKCAPALAAGCPVVVKPAED 185 Query: 196 SPLTAIRIAQLAIEAGIPAGVLNVLP-GYGHTVGKALALHMDVDTLVFTGSTKIAKQLMV 254 +PL+A+ +A+LA AG P GV NV+ G VG L + V L FTGST++ K LM Sbjct: 186 TPLSALALAELAERAGFPPGVFNVITAGDPKAVGFELTANPKVRKLSFTGSTEVGKLLMA 245 Query: 255 YAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSI 314 + +K++ LE GG +P +VF DA DL AA A ++ N G+ C +RLLV+ I Sbjct: 246 QCA-ATVKKLSLELGGNAPFMVFDDA-DLDAAVAGAMASKYRNTGQTCVCANRLLVQDGI 303 Query: 315 KDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRT 374 D F + EA+ K G L+ G L++ + + V +I GA+++ GGKR Sbjct: 304 YDAFTARLAEAVAALKVGPGLEGDFQQGPLINEEAVRKVERHIADAVAKGARVVMGGKR- 362 Query: 375 LEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIW 434 GGT+ EPTI VT M A+EE FGPV + F T EEAV +ANDT +GLAA + Sbjct: 363 -HARGGTFFEPTILADVTPDMAPAREETFGPVAPLFRFKTEEEAVRMANDTEFGLAAYFY 421 Query: 435 TSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491 + D+ + + +RA+ G V +N+ APFGG K+SG GR+ S + +E + E+K Sbjct: 422 SRDVGRVWRVSRALEYGIVGINEGLISTEVAPFGGVKESGLGREGSKYGIEDFLEVK 478 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: 575 Number of extensions: 28 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: 485 Length adjustment: 34 Effective length of query: 463 Effective length of database: 451 Effective search space: 208813 Effective search space used: 208813 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