Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__Miya:8501416 Length = 1013 Score = 221 bits (562), Expect = 1e-61 Identities = 157/477 (32%), Positives = 231/477 (48%), Gaps = 46/477 (9%) Query: 23 FINGEYTDAVSGETFECLSPVD-GRFLAKVASCDLADANRAVENARATFNSGVWSQLAPA 81 FI G+ D + +T +P +A+V + + A+E A+ F + W +PA Sbjct: 522 FIGGK--DVTTDDTIASTNPAKPAEVIARVCQGGKPEVDAAIEAAQKAFPA--WRDTSPA 577 Query: 82 KRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDE 141 R L R AD+ R+ + EL+ + L++GK QA H E ID + D Sbjct: 578 DRAMFLHRAADIARRRMFELSAWQVLEVGKQWD-----------QAFHDVGEGIDFL-DY 625 Query: 142 VAPTPHDQLGLVTR---------------EPVGVVGAIVPWNFPLLMACWKLGPALATGN 186 A H+ L L T +P G+ I PWNFP +A A+ TGN Sbjct: 626 YA---HEMLRLGTPRRMGRAPGELNHLFYQPKGIAAVIAPWNFPFAIAIGMAAAAIVTGN 682 Query: 187 SVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGST 246 V+ KPS + + ++ EAG+P GV N +PG +G L H V + FTGS Sbjct: 683 PVIFKPSSIASRIGYNLTEIFREAGLPEGVFNYVPGRSSVMGDYLVEHPQVSMICFTGSM 742 Query: 247 KIA-----KQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEV 301 ++ K V G+ KR+ E GGK+ I+ DA +A + SA F QG+ Sbjct: 743 EVGLRIQEKAAKVQPGQMQCKRVIAEMGGKNAIIIDDDADLDEAVLQVLYSAFGF-QGQK 801 Query: 302 CTAGSRLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGH 361 C+A SR++V I D+F+ +V+A + K G DP +G + D +L Y++ Sbjct: 802 CSACSRVIVLDPIYDRFVERLVKAAQAIKIGPSEDPANYMGPVADASLQKNILEYVKVAE 861 Query: 362 KDGAKLLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAI 421 ++G L+ KRT G YV TI +G+ RIAQEEIFGPVL+V+ +EA+AI Sbjct: 862 QEGKVLV---KRTDIPAEGCYVPLTIVEGIKPHHRIAQEEIFGPVLAVMRAGNFDEALAI 918 Query: 422 ANDTPYGLAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMT--APFGGFKQSGNG 476 AN T + L G+++ K R R G++++N+ G M PFGGFK SG G Sbjct: 919 ANGTRFALTGGVFSRSPENLTKARREFRVGNLYLNRGSTGAMVERQPFGGFKMSGVG 975 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: 1072 Number of extensions: 44 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: 1013 Length adjustment: 39 Effective length of query: 458 Effective length of database: 974 Effective search space: 446092 Effective search space used: 446092 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: 55 (25.8 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