Align D-3-phosphoglycerate dehydrogenase (characterized, see rationale)
to candidate WP_028949751.1 Q385_RS0100260 phosphoglycerate dehydrogenase
Query= uniprot:Q5JGC4 (304 letters) >NCBI__GCF_000619805.1:WP_028949751.1 Length = 529 Score = 265 bits (676), Expect = 2e-75 Identities = 141/309 (45%), Positives = 205/309 (66%), Gaps = 9/309 (2%) Query: 2 KVLVAAPLHEKAIEVLKNAGFEVVYEEYPDE---DRLVELVKDVDAIIVRSKPKVTRKVI 58 KVLV + K +E+L N E++ +Y E + L+E+VKD DAII RS+ VT++++ Sbjct: 3 KVLVTDDISPKGLEILNND--EMIDLDYQPEIKFNELLEIVKDYDAIITRSRTPVTKELL 60 Query: 59 EAAPKLKVIGRAGVGLDNIDLKAAEERGIKVVNSPGASSRSVAELAIGLIFAVARKIAFA 118 E A KLKV+GRAGVG+DN+DL+ A RGI V+N+PGA++ AE+ + ++AV RK+ A Sbjct: 61 ERAEKLKVVGRAGVGVDNVDLEEASRRGILVINTPGANTIGAAEITMAHLYAVLRKLHLA 120 Query: 119 DRKMREGVWAKKQCMGIELEGKTIGVVGFGRIGYQVAKIANALGMKVLFYDPYPNEERAK 178 + M EG W +K+ MG EL+GK +G++G G +G QVA A G KV+ YDPY E+ + Sbjct: 121 HKSMMEGYWDRKRFMGEELDGKVVGIIGLGNVGSQVAIRCKAAGSKVIAYDPYIPREKGE 180 Query: 179 EVGGKFAD-LETLLKESDVVTLHVPLVDATYHLINEERLKLMKPTAILINAARGAVVDTD 237 +G + D L L+K SD++TLH PL + T ++I ++ LMK IN ARG +VD D Sbjct: 181 RLGVELIDNLHDLIKMSDIITLHCPLTEETRNMIGKKEFDLMKKGVYFINCARGGIVDED 240 Query: 238 ALVKALQEGWIAGAGLDVFEEEPLPAD--HPLTKLDNVVLTPHIGASTVEAQMRAGVEVA 295 AL +A++EG IAG GLDVF +EP P D L + N+ L+PHIGA+T E+Q +++A Sbjct: 241 ALYEAVKEGKIAGLGLDVFSKEP-PDDRIRRLFEFPNISLSPHIGANTYESQDNVAIKIA 299 Query: 296 EKIVEALKG 304 + ++ ALKG Sbjct: 300 QYVIAALKG 308 Lambda K H 0.317 0.136 0.378 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: 454 Number of extensions: 30 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: 304 Length of database: 529 Length adjustment: 31 Effective length of query: 273 Effective length of database: 498 Effective search space: 135954 Effective search space used: 135954 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)
Align candidate WP_028949751.1 Q385_RS0100260 (phosphoglycerate dehydrogenase)
to HMM TIGR01327 (serA: phosphoglycerate dehydrogenase (EC 1.1.1.95))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR01327.hmm # target sequence database: /tmp/gapView.1445162.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01327 [M=525] Accession: TIGR01327 Description: PGDH: phosphoglycerate dehydrogenase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-210 684.6 0.8 5.5e-210 684.5 0.8 1.0 1 NCBI__GCF_000619805.1:WP_028949751.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000619805.1:WP_028949751.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 684.5 0.8 5.5e-210 5.5e-210 1 523 [. 3 527 .. 3 529 .] 0.98 Alignments for each domain: == domain 1 score: 684.5 bits; conditional E-value: 5.5e-210 TIGR01327 1 kvlvadklseegie.llkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaGvG 72 kvlv+d++s++g+e l +++ +++d++ +++ +elle++kdyda+i+RS+t+vt+elle+aekLkv+gRaGvG NCBI__GCF_000619805.1:WP_028949751.1 3 KVLVTDDISPKGLEiLNNDEMIDLDYQPEIKFNELLEIVKDYDAIITRSRTPVTKELLERAEKLKVVGRAGVG 75 7*************66677889*************************************************** PP TIGR01327 73 vDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygktlGviG 145 vDN+d+e+a+++Gilv+N+P +nti+aaE ++a+l a+ Rk++ a+ks+ e+ W+rk+f+G+El gk +G+iG NCBI__GCF_000619805.1:WP_028949751.1 76 VDNVDLEEASRRGILVINTPGANTIGAAEITMAHLYAVLRKLHLAHKSMMEGYWDRKRFMGEELDGKVVGIIG 148 ************************************************************************* PP TIGR01327 146 lGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelak 218 lG++Gs+va r+ka g kv+ayDPyi++ek e+lgvel+++l++l++ +D+it+H Plt+et+++igk+e++ NCBI__GCF_000619805.1:WP_028949751.1 149 LGNVGSQVAIRCKAAGSKVIAYDPYIPREKGERLGVELIDNLHDLIKMSDIITLHCPLTEETRNMIGKKEFDL 221 ************************************************************************* PP TIGR01327 219 mKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPpt..dnklleldnvvvtpHlgAsteEaqenv 289 mKkgv+ +NcaRGGi+dE+AL+ea++egk+++++lDvf+kEPp +l+e++n++++pH+gA+t+E+q+nv NCBI__GCF_000619805.1:WP_028949751.1 222 MKKGVYFINCARGGIVDEDALYEAVKEGKIAGLGLDVFSKEPPDdrIRRLFEFPNISLSPHIGANTYESQDNV 294 *******************************************944479************************ PP TIGR01327 290 avevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeese 362 a+++a+ v+ alkg++ve avN+p + +e +e++k+yl+laeklG++ +q+++++ ++++v+++G++ ++ e NCBI__GCF_000619805.1:WP_028949751.1 295 AIKIAQYVIAALKGQFVEVAVNAPFTITEGFENIKAYLELAEKLGSFLTQYAGGHFTEINVEVRGTIRDHI-E 366 *******************************************************************9877.9 PP TIGR01327 363 lltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknllevkveadkgevsvagtvleekep 435 ++++++lkg+l++vl++ vn++nA+++akergi+v s++e+ ++k+ +++++++d +ev v+gt + +k p NCBI__GCF_000619805.1:WP_028949751.1 367 PIVAFFLKGYLSPVLDTPVNIINAPFIAKERGINVVKSTREAGLNFKEFIKITAKSDGKEVVVGGTAFYDKLP 439 999********************************************************************** PP TIGR01327 436 riveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseevl 508 ri+ +d++ +d+ep g++l+++nkD+pGvigk+g++l++++iNia+++lgr ekg+ al l+lD++++e vl NCBI__GCF_000619805.1:WP_028949751.1 440 RIMLVDNYWIDIEPYGVILMFENKDVPGVIGKLGTILARHNINIAGFRLGRLEKGKIALGALQLDDKLNEAVL 512 ************************************************************************* PP TIGR01327 509 eeikevpeiksvklv 523 eei+++pei ++k v NCBI__GCF_000619805.1:WP_028949751.1 513 EEIHQLPEIIKAKQV 527 ***********9988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (525 nodes) Target sequences: 1 (529 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 22.03 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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