Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 6938534 Sama_2637 succinate-semialdehyde dehydrogenase (NAD(P)(+)) (RefSeq)
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__SB2B:6938534 Length = 480 Score = 298 bits (764), Expect = 2e-85 Identities = 176/475 (37%), Positives = 264/475 (55%), Gaps = 10/475 (2%) Query: 18 IEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQ 77 ++ + +INGE+ DA+SGET +P +A V + A+ A A + W Sbjct: 9 LKTKCYINGEWRDALSGETVTIANPATNEAIASVPVMGRDETREAIAAAEAALPA--WRA 66 Query: 78 LAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDK 137 L +R AKL R+ +L+ +N ++LAL+ T + GKP+ ++ ++ AA I W AE + Sbjct: 67 LTAKERGAKLRRWYELMLENADDLALMMTTEQGKPLAEAKG-EVVYAASFIEWFAEEAKR 125 Query: 138 VYDEVAPTPH-DQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKS 196 +Y + P D+ +V ++ VGV AI PWNFP M K GPALA G ++++KP+ ++ Sbjct: 126 LYGDTIPGHQGDKRIMVIKQGVGVTAAITPWNFPAAMITRKAGPALAAGCTMIVKPAPQT 185 Query: 197 PLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYA 256 P TA+ +A+LA EAGIP GV +V+ G +G L + V L FTGST + +LM Sbjct: 186 PFTALALAELAAEAGIPPGVFSVVTGDAVAIGNELCENPVVRKLSFTGSTGVGIKLMQQC 245 Query: 257 GESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKD 316 + +K++ LE GG +P IVF DA DL AA E A + N G+ C +RL V+ + D Sbjct: 246 APT-LKKVSLELGGNAPFIVFNDA-DLDAAVEGAMISKYRNAGQTCVCANRLYVQDGVYD 303 Query: 317 KFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLE 376 F + A+ K GN +P T G L++ + V S+++ GA L+AGGK Sbjct: 304 AFAQKLAAAVAKLKVGNGAEPGVTTGPLINAAALEKVQSHLQDALDKGATLVAGGK---- 359 Query: 377 ETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTS 436 GG ++EP I V +M++A+EE FGP+ + F ++ + ANDT +GLAA + Sbjct: 360 PLGGNFMEPAIVTNVDASMKVAREETFGPLAPLFRFSDVDDVIRQANDTEFGLAAYFYGR 419 Query: 437 DISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491 DIS K A A+ G V VN APFGG K SG GR+ S + +++Y E+K Sbjct: 420 DISLIWKVAEALEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIDEYVEIK 474 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: 568 Number of extensions: 26 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: 480 Length adjustment: 34 Effective length of query: 463 Effective length of database: 446 Effective search space: 206498 Effective search space used: 206498 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