Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate RR42_RS09460 RR42_RS09460 hypothetical protein
Query= BRENDA::A0A5H2X4C4 (538 letters) >FitnessBrowser__Cup4G11:RR42_RS09460 Length = 271 Score = 137 bits (345), Expect = 5e-37 Identities = 86/249 (34%), Positives = 130/249 (52%), Gaps = 24/249 (9%) Query: 278 LYNQAFKSAGFDGVFLHLLVDDVASFLQTYSSTDFAGFSCTIPHKEAAVKCCDEVDPVAK 337 ++N A+++ D F+ V DV +Q+ + G + ++PHK+A + D +D A+ Sbjct: 23 IHNAAYRALEIDYTFVCFGVQDVPGAVQSIRALGVRGMNVSMPHKQAVIPHLDHLDETAR 82 Query: 338 SIGAVNCIIRRQSDAKLFGYNTDYVGAISAIEDGLRGSQNGNSAGASPLNGKLFVVIGAG 397 +IGAVN I D L GYNTD +GA+ A ++ + L GK ++GAG Sbjct: 83 AIGAVNTI--NNVDGVLTGYNTDCIGAVRAFQE------------VTELQGKRIALLGAG 128 Query: 398 GAGKALGYGAKEKGARVVIANRTYDRARELAETIG---GDALSLADLENFHPEDGMILAN 454 GA +A+ YG +E GA V + NRT R ELA ++G G ALS +F D +LAN Sbjct: 129 GAARAMAYGLREAGAAVTLFNRTAARGEELAASLGLRFGGALS-----DFRAADFDLLAN 183 Query: 455 TTSIGMQPKVDETPIPKHALKHYSLVFDAVYTPKITRLLKEAEECGATIVSGLEMFIGQA 514 T+ G + D P+ H +V DA + P ++L+++A E G + G M + QA Sbjct: 184 ATAAGFRAP-DVNPVAGQLAAHL-IVMDAAFIPVRSKLIRDAAELGCRTIDGTRMMLHQA 241 Query: 515 YGQYERYTG 523 Q E YTG Sbjct: 242 CAQVEFYTG 250 Lambda K H 0.317 0.135 0.385 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: 264 Number of extensions: 12 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: 538 Length of database: 271 Length adjustment: 30 Effective length of query: 508 Effective length of database: 241 Effective search space: 122428 Effective search space used: 122428 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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