Align succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized)
to candidate WP_028311051.1 H566_RS0108130 NAD-dependent succinate-semialdehyde dehydrogenase
Query= reanno::MR1:200453 (482 letters) >NCBI__GCF_000482785.1:WP_028311051.1 Length = 484 Score = 689 bits (1777), Expect = 0.0 Identities = 336/478 (70%), Positives = 390/478 (81%) Query: 3 LNDPSLLRQQCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAALP 62 L D +L R Q I G W DA++ I +PATGA + VP MG+AET+ AIAAAE A Sbjct: 4 LKDSTLWRHQAVIGGAWLDADTGRATEILDPATGASLGTVPEMGEAETRRAIAAAEVAQK 63 Query: 63 AWRALTAKERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKGEVTYAASFIEWFAEE 122 WRAL A RG LRRW+EL+ E+ DDLA LMT+EQGKPL EAKGE+ YAASF+EWF EE Sbjct: 64 QWRALPAANRGRLLRRWYELMLEHQDDLAALMTAEQGKPLAEAKGEIAYAASFLEWFGEE 123 Query: 123 AKRIYGDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKPA 182 AKR+YGD IP D+R++V+++PVGVTAAITPWNFPAAMITRKA ALAAGC+MV+KPA Sbjct: 124 AKRLYGDVIPSPANDRRLVVVREPVGVTAAITPWNFPAAMITRKAGAALAAGCSMVIKPA 183 Query: 183 PQTPFTALALAVLAERAGIPAGVFSVITGDAIAIGNEMCTNPIVRKLSFTGSTNVGIKLM 242 PQTPF+ALAL VLAERAGIPAGV +V+TGDA+AIG E+C NP+VRKLSFTGST VGIKLM Sbjct: 184 PQTPFSALALVVLAERAGIPAGVLNVVTGDAVAIGGELCRNPVVRKLSFTGSTGVGIKLM 243 Query: 243 AQCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAGVY 302 QCAPTLKKLSLELGGNAPFIVFDDA++DAAV GAM++KYRNAGQTCVCANR+ VQ G++ Sbjct: 244 EQCAPTLKKLSLELGGNAPFIVFDDADVDAAVAGAMVSKYRNAGQTCVCANRLLVQDGIH 303 Query: 303 DEFAEKLSMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGGKVHE 362 D F KL+ AV LKVG G AGV GPLIN AAV KV+ HL DA+ KGA+V+ GGK H Sbjct: 304 DAFVAKLAEAVRTLKVGVGTEAGVNLGPLINGAAVGKVERHLADALAKGASVVTGGKPHA 363 Query: 363 LGGNFFEPTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFYGRD 422 LGGNFFEPT++T +M VAREETFGPLAP+F+F D+ I+ ANDTEFGLAAYFY RD Sbjct: 364 LGGNFFEPTIVTGVTTAMAVAREETFGPLAPVFRFTTEDEAIRMANDTEFGLAAYFYTRD 423 Query: 423 ISLVWKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIKYICM 480 I VW+V E+LEYGMVG+NTGLIS EVAPFGG+K+SGLGREGSKYG +EY EIKY+ M Sbjct: 424 IGRVWRVGEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGCDEYTEIKYLAM 481 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: 739 Number of extensions: 21 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: 484 Length adjustment: 34 Effective length of query: 448 Effective length of database: 450 Effective search space: 201600 Effective search space used: 201600 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