Align NAD-dependent succinate semialdehyde dehydrogenase (EC 1.2.1.24) (characterized)
to candidate 8502217 DvMF_2927 tartronate semialdehyde reductase (RefSeq)
Query= metacyc::MONOMER-15565 (287 letters) >FitnessBrowser__Miya:8502217 Length = 299 Score = 148 bits (374), Expect = 1e-40 Identities = 88/287 (30%), Positives = 137/287 (47%) Query: 1 MEEIGFLGIGIMGKAMAVNLLRHGFKVTVWNRTLSRCDELVQHGASVGETPAEVIKKCKY 60 M+ IGF+G+GIMG M NLL+ GF VT + R + + GA+ E+PA V Sbjct: 1 MQRIGFIGLGIMGAPMCRNLLKAGFPVTAYTRNGDKLRAMAAEGAAAAESPAAVAAASDV 60 Query: 61 TIAMLSDPAAALSVVFDKHGALEHICAGKGYIDMSTVDADTSSQISQAITSKGGSFLEAP 120 I ML + +V G E G DMS++ S +I+ + K L+AP Sbjct: 61 VITMLPNSPEVRAVALGPGGIAEGAAPGCIVADMSSIAPLASREIAAELAKKSIRMLDAP 120 Query: 121 VSGSKKPAEDGQLVILAAGDKDLYDQVVPAFDVLGKKSFFLGKIGNGAKMKLVVNMIMGS 180 VSG + A DG L ++ G ++ +D +P F + +G++G G KL +++ Sbjct: 121 VSGGEPKAIDGTLSVMVGGAQEDFDACLPVFKAMAASVVRVGEVGAGNVTKLANQIVVAG 180 Query: 181 MMNAFSEGIVLADKSGLDPHTLLDVLDLGAIANPMFKMKGPAMIKNSYPPAFPLKHQQKD 240 + A SE +VLA ++G DP + + G + + K P ++ + P F ++ KD Sbjct: 181 NIAAMSEALVLATRAGADPDLVYQAIRGGLAGSTVLDAKAPLVMDGRFTPGFRIRLHAKD 240 Query: 241 MRLALALGDENAVPMPVAAAANEAFKKARSLGLGDLDFSAVFETLSK 287 M L E VP+P+AA E + + GLGD D A+ K Sbjct: 241 MGNVLETSRELHVPLPLAAQLMEVMQGLMADGLGDADHGALIRHWEK 287 Lambda K H 0.318 0.135 0.384 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: 187 Number of extensions: 4 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: 287 Length of database: 299 Length adjustment: 26 Effective length of query: 261 Effective length of database: 273 Effective search space: 71253 Effective search space used: 71253 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: 48 (23.1 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