Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_012334470.1 M446_RS22840 shikimate dehydrogenase
Query= BRENDA::Q6PUG0 (521 letters) >NCBI__GCF_000019365.1:WP_012334470.1 Length = 285 Score = 131 bits (330), Expect = 3e-35 Identities = 100/279 (35%), Positives = 142/279 (50%), Gaps = 23/279 (8%) Query: 242 VFGLISKPVGHSKGPILHNPTFRHVGYNGIYVPMFVDD-----LKEFFRVYSSPDFAGFS 296 + GLI P+ HS P +H +G Y + + L+ FAG + Sbjct: 10 LLGLIGAPIKHSASPAMHEAAAEALGMRAHYQLIEIAGADAGLLRSLLDGVRHLGFAGVN 69 Query: 297 VGIPYKEAVVSFCDEVDPLAKSIGAVNTIIQRPCDGKLIGYNTDCEASITAIEDALKVNG 356 V PYKEAV+ D++ P A+++GAVNT++ G+LIG+NTD A+ Sbjct: 70 VTFPYKEAVLPLLDDLSPGARAVGAVNTVVVE--GGRLIGHNTDASGFGRALVQT----- 122 Query: 357 LTNGAAFLPSPLAGKLFVLVGAGGAGRALAFGAKS-RRAEIVIFDIDFDRAKALAAAVSG 415 F P+P AG + L+GAGG G+A+A EI + D D +A+ALAA++ G Sbjct: 123 ------FGPAP-AGPV-ALIGAGGVGKAIAVALSDVPGTEIRLVDTDPAKARALAASLDG 174 Query: 416 EALPFENLASFQPEKGAI-LANATPIGMHPNKDRIPVSEASLKDYVVVFDAVYTPRKTTL 474 A + + GA L N TPIGM PN+D PV L+ + V DAVY+P T L Sbjct: 175 RAEIRVCAGAEEALAGARGLVNGTPIGMLPNRDA-PVPLHLLRPDLWVADAVYSPLWTPL 233 Query: 475 LKDAEAAGAITVSGVEMFLRQAIGQFHLFTRTKAPEEFM 513 L A A GA T++G + + QA+ F LFT +AP+ M Sbjct: 234 LTAARALGAPTMTGRALAIHQALDAFRLFTGREAPQAAM 272 Lambda K H 0.320 0.138 0.405 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: 314 Number of extensions: 13 Number of successful extensions: 6 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: 521 Length of database: 285 Length adjustment: 30 Effective length of query: 491 Effective length of database: 255 Effective search space: 125205 Effective search space used: 125205 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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