Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate N515DRAFT_3581 N515DRAFT_3581 D-3-phosphoglycerate dehydrogenase
Query= BRENDA::P0A9T0 (410 letters) >FitnessBrowser__Dyella79:N515DRAFT_3581 Length = 410 Score = 520 bits (1338), Expect = e-152 Identities = 258/409 (63%), Positives = 318/409 (77%), Gaps = 1/409 (0%) Query: 3 KVSLEKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLRSR 62 K S K IK LL+EGV Q A+E R AGY+ IEFH+ +L + +LK I +AH +G+RSR Sbjct: 2 KTSYPKADIKVLLLEGVSQSAVEVFRRAGYSQIEFHEKSLPEAELKARIAEAHIVGIRSR 61 Query: 63 THLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLL 122 +HLT DV+ A +L+A+GCFCIGTNQVDL+ A ++G+PVFNAP+SNTRSVAELVI E ++ Sbjct: 62 SHLTADVLEQARRLIAVGCFCIGTNQVDLETARQQGVPVFNAPYSNTRSVAELVIAEAIM 121 Query: 123 LLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFYDI 182 LLRG+P+ NA HRG W K AAGSFE R K LGI+GYGHIGTQ+G+LAESLGM V F+DI Sbjct: 122 LLRGIPQKNALCHRGGWTKSAAGSFEVRDKVLGIVGYGHIGTQVGVLAESLGMRVIFHDI 181 Query: 183 ENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGT 242 E KL LGNA L DLL +DVV+LHVPE P+TK M+GA E++ M+ G+ LINASRGT Sbjct: 182 ETKLSLGNARAAGSLDDLLERADVVTLHVPETPATKLMIGATELAKMRKGAALINASRGT 241 Query: 243 VVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEAQE 302 VVDI AL AL + H+AGAA+DVFP EP N DPF SPL DNV+LTPHIGGST EAQ+ Sbjct: 242 VVDIDALAAALRTGHVAGAAVDVFPLEPKGNDDPFVSPLVGMDNVILTPHIGGSTLEAQD 301 Query: 303 NIGLEVAGKLIKYSDNGSTLSAVNFPEVSLPLH-GGRRLMHIHENRPGVLTALNKIFAEQ 361 NIG+EVA KL++YSDNGSTLSAVNFPEV+LP H RRL+HIH N PGVL+ +N++F+ Sbjct: 302 NIGIEVASKLVRYSDNGSTLSAVNFPEVTLPEHPNSRRLLHIHRNVPGVLSRINELFSAG 361 Query: 362 GVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARLLY 410 +NI AQ+LQT +Q+GYVVID+ ADE A + AIPGT+R+R+LY Sbjct: 362 NINIDAQFLQTDSQVGYVVIDVSADEAQAGALKDRLAAIPGTLRSRVLY 410 Lambda K H 0.318 0.135 0.383 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: 516 Number of extensions: 15 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: 410 Length of database: 410 Length adjustment: 31 Effective length of query: 379 Effective length of database: 379 Effective search space: 143641 Effective search space used: 143641 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 (21.7 bits) S2: 50 (23.9 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