Align Shikimate dehydrogenase-like protein HI_0607; SDH-L; EC 1.1.1.25 (characterized)
to candidate BWI76_RS01715 BWI76_RS01715 shikimate 5-dehydrogenase
Query= SwissProt::P44774 (271 letters) >FitnessBrowser__Koxy:BWI76_RS01715 Length = 269 Score = 335 bits (858), Expect = 8e-97 Identities = 169/268 (63%), Positives = 205/268 (76%) Query: 1 MINKDTQLCMSLSGRPSNFGTTFHNYLYDKLGLNFIYKAFTTQDIEHAIKGVRALGIRGC 60 MIN+DTQLCMSL+GRP NFGT FHNYLY+KLGLN+IYKAFTTQDI A+ GVRALG+RGC Sbjct: 1 MINRDTQLCMSLAGRPGNFGTRFHNYLYEKLGLNYIYKAFTTQDIAAAVNGVRALGVRGC 60 Query: 61 AVSMPFKETCMPFLDEIHPSAQAIESVNTIVNDNGFLRAYNTDYIAIVKLIEKYHLNKNA 120 AVSMPFKE+C+PFLD + PSA+ I+SVNTIVND+G L NTDYIA+ LI+ + L+ +A Sbjct: 61 AVSMPFKESCIPFLDALDPSAKVIDSVNTIVNDDGRLTGLNTDYIAVKSLIDSHRLDASA 120 Query: 121 KVIVHGSGGMAKAVVAAFKNSGFEKLKIYARNVKTGQYLAALYGYAYINSLENQQADILV 180 KV++ GSGGM KAV+AAF+++GF + I AR+ + G LA YG+ + E ADILV Sbjct: 121 KVMIQGSGGMGKAVIAAFRDAGFRDVIIAARHRERGLALAKQYGFQWQPRPEGMAADILV 180 Query: 181 NVTSIGMKGGKEEMDLAFPKAFIDNASVAFDVVAMPVETPFIRYAQARGKQTISGAAVIV 240 NVT +GM GG E LAF + ++ A+V FDVVA+P ETP IR AQ K+ ISGA VI Sbjct: 181 NVTPLGMAGGAESETLAFSQTMVERAAVVFDVVALPPETPLIRLAQRLDKRVISGAEVIA 240 Query: 241 LQAVEQFELYTHQRPSDELIAEAAAFAR 268 LQAVEQF LYT RP L+AEAAAFAR Sbjct: 241 LQAVEQFALYTGVRPDAALVAEAAAFAR 268 Lambda K H 0.321 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: 233 Number of extensions: 5 Number of successful extensions: 1 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: 271 Length of database: 269 Length adjustment: 25 Effective length of query: 246 Effective length of database: 244 Effective search space: 60024 Effective search space used: 60024 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 (21.9 bits) S2: 47 (22.7 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