Align succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized)
to candidate GFF3587 Psest_3654 succinate-semialdehyde dehydrogenase
Query= reanno::MR1:200453 (482 letters) >FitnessBrowser__psRCH2:GFF3587 Length = 488 Score = 737 bits (1902), Expect = 0.0 Identities = 361/481 (75%), Positives = 413/481 (85%), Gaps = 3/481 (0%) Query: 3 LNDPSLLRQQCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAALP 62 L P LLRQ Y+NG+WC+A+S I NPATG +I VP MG+ ET+ AI AA+AA P Sbjct: 5 LGQPDLLRQTAYLNGEWCEADSGARTEIFNPATGELIGAVPNMGRGETRRAIEAAQAAQP 64 Query: 63 AWRALTAKERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKGEVTYAASFIEWFAEE 122 AWRALTAKER A+LRRW+EL+ EN +DLA +MT+EQGKPL EA+GEV YAASF+EWFAEE Sbjct: 65 AWRALTAKERAARLRRWYELMLENQEDLARIMTAEQGKPLAEARGEVAYAASFLEWFAEE 124 Query: 123 AKRIYGDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKPA 182 KR+YGD IP H GDKRI+V K+PVGVTAAITPWNFP+AMITRKA PALAAGC MV+KPA Sbjct: 125 GKRLYGDVIPAHAGDKRILVQKEPVGVTAAITPWNFPSAMITRKAGPALAAGCAMVLKPA 184 Query: 183 PQTPFTALALAVLAERAGIPAGVFSVITGDAIA---IGNEMCTNPIVRKLSFTGSTNVGI 239 PQTPF+ALALA LAERAGIPAG+ SVIT DA +G E+C NPIVRKLSFTGST VGI Sbjct: 185 PQTPFSALALAALAERAGIPAGLLSVITADAATSREVGAELCENPIVRKLSFTGSTAVGI 244 Query: 240 KLMAQCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQA 299 KLM QCAPTLKKLSLELGGNAPFIVFDDA++DAAVEGAMI+KYRNAGQTCVCANRIYVQ Sbjct: 245 KLMQQCAPTLKKLSLELGGNAPFIVFDDADLDAAVEGAMISKYRNAGQTCVCANRIYVQD 304 Query: 300 GVYDEFAEKLSMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGGK 359 G+YD F +KLS AVA+LKVG G GVTTGPLI+AAAV KVQ HL+DA+ KGAT+LAGGK Sbjct: 305 GIYDAFVDKLSAAVARLKVGNGAEEGVTTGPLIDAAAVAKVQRHLQDALDKGATLLAGGK 364 Query: 360 VHELGGNFFEPTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFY 419 H LGGNFFEPT++ M VAREETFGPLAPLF+F D D+VI+QANDTEFGLAAYFY Sbjct: 365 PHALGGNFFEPTLVGGVTSEMAVAREETFGPLAPLFRFRDEDEVIRQANDTEFGLAAYFY 424 Query: 420 GRDISLVWKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIKYIC 479 RD+S V++VAE+LEYGMVG+NTG+ISTEVAPFGGMK+SGLGREGSKYG++EY+EIKY+C Sbjct: 425 ARDLSRVFRVAEALEYGMVGINTGVISTEVAPFGGMKASGLGREGSKYGLDEYVEIKYLC 484 Query: 480 M 480 + Sbjct: 485 L 485 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: 757 Number of extensions: 17 Number of successful extensions: 2 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: 488 Length adjustment: 34 Effective length of query: 448 Effective length of database: 454 Effective search space: 203392 Effective search space used: 203392 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 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