Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate N515DRAFT_3581 N515DRAFT_3581 D-3-phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >FitnessBrowser__Dyella79:N515DRAFT_3581 Length = 410 Score = 423 bits (1088), Expect = e-123 Identities = 212/409 (51%), Positives = 292/409 (71%), Gaps = 3/409 (0%) Query: 225 KFSYPKSRINVLLLENVHPIGVEIMKQEGYN-VEVVSSAMSEEELCEKIKNVSIIGIRSK 283 K SYPK+ I VLLLE V VE+ ++ GY+ +E ++ E EL +I I+GIRS+ Sbjct: 2 KTSYPKADIKVLLLEGVSQSAVEVFRRAGYSQIEFHEKSLPEAELKARIAEAHIVGIRSR 61 Query: 284 TQITKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIF 343 + +T VLE A RL+AVG FCIGTNQ+DLET +++G+ VFNAP+SNTRSV EL I+E I Sbjct: 62 SHLTADVLEQARRLIAVGCFCIGTNQVDLETARQQGVPVFNAPYSNTRSVAELVIAEAIM 121 Query: 344 LMRNLHDKTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYDI 403 L+R + K H+G W KSA+GSFEVR K LGI+GYG+IG Q+ VLAE++GM V ++DI Sbjct: 122 LLRGIPQKNALCHRGGWTKSAAGSFEVRDKVLGIVGYGHIGTQVGVLAESLGMRVIFHDI 181 Query: 404 VERLALGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGH 463 +L+LGNA SLD+LLE D+++LHV K ++ ++ KM+KGA L+N SRG Sbjct: 182 ETKLSLGNARAAGSLDDLLERADVVTLHVPETPATKLMIGATELAKMRKGAALINASRGT 241 Query: 464 VVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQE 523 VVD+ AL AL +GH+AGAAVDVFP EPK ND+PF S L+G N ILTPHIGGSTLEAQ+ Sbjct: 242 VVDIDALAAALRTGHVAGAAVDVFPLEPKGNDDPFVSPLVGMDNVILTPHIGGSTLEAQD 301 Query: 524 NIAQFVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLASY 583 NI V K++ Y ++G+T ++VNFP + LP ++ RL+HIH+N PGVL++IN++ ++ Sbjct: 302 NIGIEVASKLVRYSDNGSTLSAVNFPEVTLPEHPNSRRLLHIHRNVPGVLSRINELFSAG 361 Query: 584 KINIVGQYLKTNEKIGYVITDI--DKRYSNDVIDALKEIEGTIRFRILY 630 INI Q+L+T+ ++GYV+ D+ D+ + + D L I GT+R R+LY Sbjct: 362 NINIDAQFLQTDSQVGYVVIDVSADEAQAGALKDRLAAIPGTLRSRVLY 410 Lambda K H 0.317 0.136 0.377 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: 607 Number of extensions: 17 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: 630 Length of database: 410 Length adjustment: 34 Effective length of query: 596 Effective length of database: 376 Effective search space: 224096 Effective search space used: 224096 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: 52 (24.6 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