Align succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized)
to candidate WP_066609128.1 V473_RS20300 NAD-dependent succinate-semialdehyde dehydrogenase
Query= reanno::MR1:200453 (482 letters) >NCBI__GCF_001046645.1:WP_066609128.1 Length = 487 Score = 579 bits (1492), Expect = e-170 Identities = 289/476 (60%), Positives = 362/476 (76%) Query: 1 MLLNDPSLLRQQCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAA 60 ++L++P+L ++ +I G W A S TV + NPATGA+I VP G+A+T AAIAAAEAA Sbjct: 3 LILDNPALFIERAFIGGAWVGATSGATVPVDNPATGAIIGTVPDCGEADTLAAIAAAEAA 62 Query: 61 LPAWRALTAKERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKGEVTYAASFIEWFA 120 PAW+A TA +R A L RW L+ N DL +MT+EQGKP+ EA+GE+ YAASFI+WFA Sbjct: 63 FPAWKAQTAGDRAAVLERWHALVLANVADLGRIMTAEQGKPIAEAEGEIRYAASFIKWFA 122 Query: 121 EEAKRIYGDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVK 180 EE +R+ G +P + ++RI+V+K+PVGV+AAITPWNFPAAMITRK APALAAGC +VVK Sbjct: 123 EEGRRVDGGIVPAPEANRRILVMKEPVGVSAAITPWNFPAAMITRKCAPALAAGCPVVVK 182 Query: 181 PAPQTPFTALALAVLAERAGIPAGVFSVITGDAIAIGNEMCTNPIVRKLSFTGSTNVGIK 240 P+ TPFTALALA LAE AGIPAGVF+++TG AIG + +P+VRKLSFTGST VG Sbjct: 183 PSELTPFTALALAKLAEEAGIPAGVFNIVTGLPTAIGGALTASPVVRKLSFTGSTRVGSL 242 Query: 241 LMAQCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAG 300 LM QCA T+K++S ELGGNAP IVFDDA++D AV AM++K+RNAGQTCVCANRI VQ G Sbjct: 243 LMRQCADTIKRVSFELGGNAPLIVFDDADVDIAVASAMVSKFRNAGQTCVCANRILVQDG 302 Query: 301 VYDEFAEKLSMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGGKV 360 VYD+FAEKL+ AV+ LKV G G T GPLIN AAVEKVQ+H+EDA+ GAT+ A Sbjct: 303 VYDQFAEKLARAVSALKVAPGDRTGSTIGPLINVAAVEKVQAHVEDALSHGATLFAQAAN 362 Query: 361 HELGGNFFEPTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFYG 420 G F P +LT A + MR+A+EETFGP+APLF+F ++ I+ AN T +GLAAYFY Sbjct: 363 DATGARFATPVILTGATRDMRLAQEETFGPVAPLFRFTHEEEGIELANATSYGLAAYFYT 422 Query: 421 RDISLVWKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIK 476 ++ ++VAE LE GMV +N+G I+ EVAPFGG+K SGLGREG+ GIEEYLE K Sbjct: 423 ENLHRAFRVAERLEAGMVALNSGAIAMEVAPFGGVKMSGLGREGAHAGIEEYLETK 478 Lambda K H 0.318 0.133 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: 668 Number of extensions: 23 Number of successful extensions: 1 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: 482 Length of database: 487 Length adjustment: 34 Effective length of query: 448 Effective length of database: 453 Effective search space: 202944 Effective search space used: 202944 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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