Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 208845 DVU3319 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >MicrobesOnline__882:208845 Length = 1006 Score = 211 bits (538), Expect = 7e-59 Identities = 145/433 (33%), Positives = 213/433 (49%), Gaps = 24/433 (5%) Query: 55 DLADANRAVENARATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIG 114 ++ DA A + A T W +PA R A L R AD+ RK + EL+ + +++GK Sbjct: 549 EIDDAIAAAKKAALT-----WRDTSPADRAAYLRRAADICRKRIWELSAWQVVEVGKQ-W 602 Query: 115 DSSSIDIPGAAQAIHWTAEAIDKVYDEV----APTPHDQLGLVTREPVGVVGAIVPWNFP 170 D + D+ + + A + ++ AP H+ L +P G+ I PWNFP Sbjct: 603 DQAYHDVTEGIDFLEYYAREMLRLGAPRRMGRAPGEHNHLFY---QPKGIAAVIAPWNFP 659 Query: 171 LLMACWKLGPALATGNSVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKA 230 +A A+ TGN V+ KPS S +A++ EAG+P GV N PG +G Sbjct: 660 FAIAIGMASAAIVTGNPVIFKPSSISSRIGYNLAEVFREAGLPEGVFNYCPGRSSIMGDY 719 Query: 231 LALHMDVDTLVFTGSTKIA-----KQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQA 285 L H D+ + FTGS ++ K V G+ KR+ E GGK+ I+ DA +A Sbjct: 720 LVEHPDISLICFTGSMEVGLRIQEKAAKVQPGQRQCKRVIAEMGGKNATIIDDDADLDEA 779 Query: 286 AAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALV 345 + SA F QG+ C+A SR++V +I D+F+ +V+A G DP +G + Sbjct: 780 VLQVLYSAFGF-QGQKCSACSRVIVLDAIYDRFIERLVKAASSIHIGPSEDPSNYMGPVA 838 Query: 346 DTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGP 405 D V YI ++G LL KRT G YV TI + RIAQEEIFGP Sbjct: 839 DATLQKNVSDYIRIAEEEGRVLL---KRTDLPAEGCYVPLTIVGDIRPEHRIAQEEIFGP 895 Query: 406 VLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMT- 464 VL+V+ T +EA++IAN T + L +++ K R R G++++N+ G + Sbjct: 896 VLAVMRAATFDEALSIANGTRFALTGAVFSRSPEHLDKARREFRVGNLYLNKGSTGALVE 955 Query: 465 -APFGGFKQSGNG 476 PFGGF SG G Sbjct: 956 RQPFGGFAMSGVG 968 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: 1019 Number of extensions: 47 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: 1006 Length adjustment: 39 Effective length of query: 458 Effective length of database: 967 Effective search space: 442886 Effective search space used: 442886 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: 54 (25.4 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