Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate CCNA_03242 CCNA_03242 succinic semialdehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__Caulo:CCNA_03242 Length = 485 Score = 301 bits (772), Expect = 3e-86 Identities = 183/477 (38%), Positives = 272/477 (57%), Gaps = 13/477 (2%) Query: 18 IEGRAFINGEYTDAVSGE-TFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWS 76 +E A I+G++ V GE +F+ L+P DG +A VA A+ A++ A + W+ Sbjct: 10 VETAALIDGQW---VRGEASFDVLNPADGTLIAAVADLGAAETTLAIDAAHRALPA--WA 64 Query: 77 QLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAID 136 +R A L R++DL+ + ++LA L T + GKP+ ++ + GA+ I W AE Sbjct: 65 ARTAKERGAILRRWSDLILAHADDLARLMTDEQGKPLAEAKGEVVYGAS-FIDWFAEEAK 123 Query: 137 KVYDEVAPTPHDQLGLVT-REPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEK 195 + Y PTP L + ++PVGV AI PWNFP+ M K+GPALA G +VV+KP+ + Sbjct: 124 RAYGHTIPTPMPGKRLASIKQPVGVCAAIAPWNFPIAMITRKVGPALAAGCTVVVKPAAE 183 Query: 196 SPLTAIRIAQLAIEAGIPAGVLNVLPGYGHT-VGKALALHMDVDTLVFTGSTKIAKQLMV 254 +PL+A+ IA+LA EAG+PAGVLN++ + VGK L V L FTGST I K L Sbjct: 184 TPLSALAIARLATEAGVPAGVLNIVTTTRSSEVGKVLCDDSRVRKLSFTGSTPIGKVLYQ 243 Query: 255 YAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSI 314 MK++ LE GG +P IVF DA DL+AA + A ++ N G+ C +RL+V+ I Sbjct: 244 QCA-GTMKKLSLELGGNAPFIVFDDA-DLEAAVDGAIASKYRNAGQTCVCANRLIVQSGI 301 Query: 315 KDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRT 374 D F + E + K G +G L++ + + V+ + + GA++L GG Sbjct: 302 HDAFAARLAEKVAALKVGPGTGEGVQIGPLINEKALTKVVGLVSGAVQAGAEVLTGGD-- 359 Query: 375 LEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIW 434 + GG + +PT+ G T MRI QEEIFGPV ++ F+T EAV +AN TP+GLAA + Sbjct: 360 VHGLGGHFYQPTVLVGATPEMRIFQEEIFGPVAPIVKFETEAEAVELANATPFGLAAYFY 419 Query: 435 TSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491 + D+ + + A + AG V +N+ APFGG K+SG GR+ + L++Y E K Sbjct: 420 SRDVGRCWRVAEQIEAGMVGINEGLISTEVAPFGGVKESGLGREGASEGLDEYLETK 476 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: 604 Number of extensions: 29 Number of successful extensions: 8 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