Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_034997912.1 DL88_RS15090 shikimate dehydrogenase
Query= BRENDA::Q6PUG0 (521 letters) >NCBI__GCF_000745425.1:WP_034997912.1 Length = 291 Score = 112 bits (279), Expect = 2e-29 Identities = 91/296 (30%), Positives = 145/296 (48%), Gaps = 31/296 (10%) Query: 240 TKVFGLISKPVGHSKGPILHNPTFRHVGYNGIYVPMFVD--DLKEFFRVYSSPDFAGFSV 297 T++ LI+ P+ HS P +HN +G + Y+ VD DL++ R G++V Sbjct: 11 TELLALIAYPIRHSDSPRMHNLALAKLGLDYAYLAFEVDAPDLEDAIRALRVLKVRGWNV 70 Query: 298 GIPYKEAVVSFCDEVDPLAKSIGAVNTIIQRPCDGKLIGYNTDCEASITAIEDALKVNGL 357 +P K V+ + D + A+ IGA NTI+ +G L G NTD + A+ + G+ Sbjct: 71 SMPNKMEVIKYLDHISTAAELIGACNTIVND--NGVLRGENTDGLGYMAALRE----QGV 124 Query: 358 TNGAAFLPSPLAGKLFVLVGAGGAGRALAF-GAKSRRAEIVIF---DIDFDRAKALAAAV 413 K L+GAGGA A+A A A I IF D F + +A AA + Sbjct: 125 ET---------RDKKITLIGAGGAAMAIATQAALDGVASIHIFNRRDDFFAKGEANAAKI 175 Query: 414 SGEALP------FENLASFQP--EKGAILANATPIGMHPNKDRI-PVSEAS-LKDYVVVF 463 S + ++L +F + A+LANAT +G + + P+ + L+ + V Sbjct: 176 SEKTNAKVSLHDLDDLETFHACVKDSAVLANATNVGFKGKLEGLSPLPDPGVLRPDLFVT 235 Query: 464 DAVYTPRKTTLLKDAEAAGAITVSGVEMFLRQAIGQFHLFTRTKAPEEFMRDIVMA 519 D++Y PRKT L+ AEAAG T++G+ M L Q F ++T P ++++D + A Sbjct: 236 DSIYAPRKTKFLEQAEAAGCRTMNGIPMMLHQGAAAFKMWTGNDMPLDYVKDHLFA 291 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: 295 Number of extensions: 14 Number of successful extensions: 3 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: 291 Length adjustment: 30 Effective length of query: 491 Effective length of database: 261 Effective search space: 128151 Effective search space used: 128151 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