Align NAD-dependent succinate semialdehyde dehydrogenase (EC 1.2.1.24) (characterized)
to candidate 8501602 DvMF_2320 6-phosphogluconate dehydrogenase NAD-binding (RefSeq)
Query= metacyc::MONOMER-15565 (287 letters) >FitnessBrowser__Miya:8501602 Length = 287 Score = 149 bits (375), Expect = 9e-41 Identities = 93/283 (32%), Positives = 142/283 (50%), Gaps = 4/283 (1%) Query: 1 MEEIGFLGIGIMGKAMAVNLLRHGFKVTVWNRTLSRCDELVQHGASVGETPAEVIKKCKY 60 M I LG+G MG+ MA NLL+ G +VTVWNRT + L+ GA+ TP + + Sbjct: 1 MSHIAVLGLGAMGRRMAANLLKAGHQVTVWNRTARAAEPLLALGATQAATPKQAAAGADF 60 Query: 61 TIAMLSDPAAALSVVFDKH-GALEHICAGKGYIDMSTVDADTSSQISQAITSKGGSFLEA 119 +AM+ D AA+ +V D GA + G +D ST+ D ++ ++G + LE Sbjct: 61 VLAMVRDDAASATVWLDAETGAFAGMRPGAIAMDSSTLSVDWIKKLGAEAANRGVTLLET 120 Query: 120 PVSGSKKPAEDGQLVILAAGDKDLYDQVVPAFDVLGKKSFFLGKIGNGAKMKLVVNMIMG 179 PVSGS A+ QL+ L G D Q P +G G IG GA KL N ++G Sbjct: 121 PVSGSLPQADAAQLIFLVGGSADACRQAEPVLLAMGSAVNHTGDIGAGALTKLATNALLG 180 Query: 180 SMMNAFSEGIVLADKSGLDPHTLLDVLDLGAIANPMFKMKGPAMIKNSYPPAFPLKHQQK 239 + A +E I + ++G D ++ ++ A+ +P + A++ P FP++ +K Sbjct: 181 VQVTAIAELIGMLRRNGADAQKIMGIIAGTAVWSPYAQRAIGALLSGEAPVMFPVELVEK 240 Query: 240 DMRLAL-ALGDENAVPMPVAAAANEAFKKARSLGLGDLDFSAV 281 D AL A G +A P AAA F++ GLGD + ++V Sbjct: 241 DFGYALEAAGSPDAA--PTIAAARSVFRRGMDKGLGDANLTSV 281 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: 177 Number of extensions: 7 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: 287 Length of database: 287 Length adjustment: 26 Effective length of query: 261 Effective length of database: 261 Effective search space: 68121 Effective search space used: 68121 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: 47 (22.7 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