Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate HSERO_RS22255 HSERO_RS22255 3-phosphoglycerate dehydrogenase
Query= uniprot:Q6LWW6 (523 letters) >FitnessBrowser__HerbieS:HSERO_RS22255 Length = 308 Score = 206 bits (523), Expect = 1e-57 Identities = 114/296 (38%), Positives = 186/296 (62%), Gaps = 9/296 (3%) Query: 10 LHESAVEILKQAGEVEVATGLTVEELKLKIKDVD---ALVIRSGTTATREIIEASENLKV 66 L ++AVE+L+ E+ A E+ +K+ + A+++R G + R +++A+ L+V Sbjct: 16 LAQAAVELLRDY-ELVYAGAKPTEDDMVKLAQLHQPVAIIVRYGGVSAR-VMDAAPILRV 73 Query: 67 IARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAAARNIPQATASIKSGK 126 I++ G G+D++D AA ++GI V A A++ +VAE + +++A A+N+ ++ G Sbjct: 74 ISKHGTGIDSIDSQAAQQRGIAVKAAAGANAPAVAEHTWALIMACAKNVVGLDQRMREGH 133 Query: 127 WDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVASELGIKLLT 186 WD+ + K +E+ G+TLG+VGLG IG++VA A A GM ++A+DPY E + G++L+ Sbjct: 134 WDKSTHKSLELQGRTLGLVGLGAIGRRVAAVAAALGMPVLAHDPYAKE---APQGVQLVD 190 Query: 187 VDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNCARGGLIDEAALYDALNSG 246 +D L SD ++LH PLT + KHMI + +A MK +++N ARGGLIDE AL AL+SG Sbjct: 191 LDTLFAQSDVVSLHCPLTAENKHMINAQSLARMKDGAILVNTARGGLIDEQALIAALDSG 250 Query: 247 KIKAAALDVFEQEP-PKESPLLTLNNLIGTPHQGASTEEAQLSAGTIVAEQTVKIL 301 K++AA LD FE+EP PL + N + +PH G T +A ++ GT A + +L Sbjct: 251 KLRAAGLDSFEKEPFTAPHPLQRVGNAVLSPHIGGVTSDAYIAMGTGAASNVLAVL 306 Lambda K H 0.316 0.134 0.364 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: 321 Number of extensions: 19 Number of successful extensions: 2 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: 523 Length of database: 308 Length adjustment: 31 Effective length of query: 492 Effective length of database: 277 Effective search space: 136284 Effective search space used: 136284 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