Align Shikimate 5-dehydrogenase (characterized, see rationale)
to candidate CA265_RS19745 CA265_RS19745 shikimate dehydrogenase
Query= uniprot:Q8A006_BACTN (248 letters) >FitnessBrowser__Pedo557:CA265_RS19745 Length = 247 Score = 242 bits (618), Expect = 4e-69 Identities = 128/249 (51%), Positives = 167/249 (67%), Gaps = 3/249 (1%) Query: 1 MEKYGLIGYPLRHSFSIGYFNEKFRSEGINA-EYVNFEIPNINDFMEVIEENPNLCGLNV 59 M+ YGLIGYPL HSFS YF EKF++EGI +Y F I +I +++ ENP+LCGLNV Sbjct: 1 MKTYGLIGYPLSHSFSKKYFTEKFQNEGIAGHQYELFPIADIKSLPDLLNENPSLCGLNV 60 Query: 60 TIPYKEQVIPFLNELDRDTAKIGAVNVIKIIRQPKGKVKLVGYNSDIIGFTQSIQPLLQP 119 TIP+K V+ +LNE+D KIGAVN I I + +GK L GYN+D GF +S++PLL P Sbjct: 61 TIPHKVNVLCYLNEVDEAAEKIGAVNCISI-KSFEGKNYLKGYNTDAYGFEESLKPLLGP 119 Query: 120 QHKKALILGTGGASKAVYHGLKNLGIESVFVSRTHKTDDMLTYEELTPEIMEEYTVIVNC 179 QH KAL+ G GGA+KAV + L+ L I+ V RT +L Y E++PEI+ + +++N Sbjct: 120 QHTKALVFGDGGAAKAVKYVLEKLNIQYQLVVRTAVPGAIL-YSEVSPEILASHQLLINT 178 Query: 180 TPVGMYPKVDFCPNIPYELLTPNHLLYDLLYNPNVTLFMKKGEAQGAVTKNGLEMLLLQA 239 TP+GM P VD P I Y LL P +L YDL+YNP T F+ K +GA KNGLEML QA Sbjct: 179 TPLGMSPNVDTFPEIDYSLLGPGYLAYDLVYNPLETAFLAKAAERGAAIKNGLEMLYKQA 238 Query: 240 FAAWEIWHR 248 AW IW++ Sbjct: 239 EKAWAIWNK 247 Lambda K H 0.320 0.140 0.419 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: 239 Number of extensions: 12 Number of successful extensions: 4 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: 248 Length of database: 247 Length adjustment: 24 Effective length of query: 224 Effective length of database: 223 Effective search space: 49952 Effective search space used: 49952 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: 46 (22.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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