Align phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized)
to candidate GFF3560 PGA1_c36140 D-3-phosphoglycerate dehydrogenase SerA
Query= CharProtDB::CH_004924 (525 letters) >FitnessBrowser__Phaeo:GFF3560 Length = 531 Score = 403 bits (1036), Expect = e-117 Identities = 210/501 (41%), Positives = 312/501 (62%), Gaps = 5/501 (0%) Query: 3 RVLVSDKMSNDGLQPLIESDFIEIVQKNVADAEDELHT----FDALLVRSATKVTEDLFN 58 +VL+SDK+S +Q + Q ++ +D+L +D L +RSATKVT+ + + Sbjct: 4 KVLISDKLSEAAVQIFRDRGIDVDFQPDLGKDKDKLAAIIGDYDGLAIRSATKVTQKILD 63 Query: 59 KMTSLKIVGRAGVGVDNIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQAN 118 T+LK++ RAG+G DNID D A++ GVIV+N P GN I+TAEH AM+ ++ R IP+A+ Sbjct: 64 NATNLKVIARAGIGTDNIDKDAASQKGVIVMNTPFGNMITTAEHAIAMMFAVARQIPEAS 123 Query: 119 ISVKSREWNRTAYVGSELYGKTLGIVGLGRIGSEIAQRRGAFGMTVHVFDPFLTEERAKK 178 S + +W ++ ++G EL KTLG++G G IG + R M V +DPFL++E+A K Sbjct: 124 ASTHAGKWEKSKFMGVELTNKTLGVIGAGNIGGIVCDRARGLKMKVVAYDPFLSQEKADK 183 Query: 179 IGVNSRTFEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEAAL 238 IGV +E+L AD IT+H PLT +T+ +L+KE + KTKKGVR+INCARGG++DEAAL Sbjct: 184 IGVEKVELDELLARADFITLHVPLTDQTRNILSKENLEKTKKGVRIINCARGGLVDEAAL 243 Query: 239 LEALENGHVAGAALDVFEVEPPVDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSEEVLQ 298 E L +GHVAGAA DVF EP N L P V+ TPHLGA+T EAQ NVA QV+E++ Sbjct: 244 AELLTSGHVAGAAFDVFSEEPAKTNPLFGLPNVVCTPHLGAATSEAQENVALQVAEQMSN 303 Query: 299 FAKGLPVMSAINLPAMTKDEFAKIKPYHQIAGKIGSLVSQCMKEPVQDVAIQYEGTIAKL 358 + V +A+N+P+MT +E + P+ ++G +G + Q EP+Q + I Y+G +++ Sbjct: 304 YLLDGAVENALNMPSMTAEEARVMGPWVALSGHLGGFIGQMTDEPIQAINILYDGVASEM 363 Query: 359 ETSFITKALLSGFLKPRVDSTVNEVNAGGVAKERGISFSEKISSSESGYDNCISVKVTGD 418 + + ++++G +K +++ VN V+A VA+ERGI S +D I V V Sbjct: 364 NLAALNCSVVAGIMK-KLNPDVNMVSAPVVARERGIQISTTNQDKSGTFDGYIKVTVVTS 422 Query: 419 RSTFTVTATYIPHFGERIVEINGFNIDFYPTGHLVYIQHQDTTGVIGRVGRILGDNDINI 478 + +V T R ++I G NID H++Y ++D G+IG +G+ILGD +NI Sbjct: 423 KRERSVAGTVFSDGKPRFIQIKGINIDAEVGAHMLYTTNEDVPGIIGTLGQILGDMGVNI 482 Query: 479 ATMQVGRKEKGGEAIMMLSFD 499 A +GR E GGEAI +L D Sbjct: 483 ANFTLGRSEAGGEAIALLYVD 503 Lambda K H 0.317 0.134 0.374 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: 615 Number of extensions: 20 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: 525 Length of database: 531 Length adjustment: 35 Effective length of query: 490 Effective length of database: 496 Effective search space: 243040 Effective search space used: 243040 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)
Align candidate GFF3560 PGA1_c36140 (D-3-phosphoglycerate dehydrogenase SerA)
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.21950.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-203 663.2 5.4 1.7e-203 663.0 5.4 1.0 1 lcl|FitnessBrowser__Phaeo:GFF3560 PGA1_c36140 D-3-phosphoglycerate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF3560 PGA1_c36140 D-3-phosphoglycerate dehydrogenase SerA # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 663.0 5.4 1.7e-203 1.7e-203 1 521 [. 4 524 .. 4 528 .. 0.98 Alignments for each domain: == domain 1 score: 663.0 bits; conditional E-value: 1.7e-203 TIGR01327 1 kvlvadklseegiellkekelevdvktgl..skeellekikdydalivRSatkvteelleaaekLkvigRaGvGvD 74 kvl++dklse++++++++++++vd + +l +k++l ++i dyd+l +RSatkvt+++l++a++Lkvi+RaG+G D lcl|FitnessBrowser__Phaeo:GFF3560 4 KVLISDKLSEAAVQIFRDRGIDVDFQPDLgkDKDKLAAIIGDYDGLAIRSATKVTQKILDNATNLKVIARAGIGTD 79 7*************************998335678999************************************** PP TIGR01327 75 NidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygktlGviGlGriG 150 Nid +aa++kG++v+N+P gn i++aE+a+a+++a+aR+ip+a +s++++kWe++kf+G+El++ktlGviG+G+iG lcl|FitnessBrowser__Phaeo:GFF3560 80 NIDKDAASQKGVIVMNTPFGNMITTAEHAIAMMFAVARQIPEASASTHAGKWEKSKFMGVELTNKTLGVIGAGNIG 155 **************************************************************************** PP TIGR01327 151 sevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelakmKkgviiv 226 +v +ra++l+mkv+ayDP++s+eka+k+gve+++ ldella+aD+it+HvPlt++t+++++ke+l+k+Kkgv+i+ lcl|FitnessBrowser__Phaeo:GFF3560 156 GIVCDRARGLKMKVVAYDPFLSQEKADKIGVEKVE-LDELLARADFITLHVPLTDQTRNILSKENLEKTKKGVRII 230 ********************************666.**************************************** PP TIGR01327 227 NcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpHlgAsteEaqenvavevaeevlealk 302 NcaRGG++dE+AL+e+l++g+v++aa+Dvf++EP++ n+l+ l+nvv tpHlgA t+Eaqenva++vae+++++l lcl|FitnessBrowser__Phaeo:GFF3560 231 NCARGGLVDEAALAELLTSGHVAGAAFDVFSEEPAKTNPLFGLPNVVCTPHLGAATSEAQENVALQVAEQMSNYLL 306 **************************************************************************** PP TIGR01327 303 gevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeeselltsallkgllkevle 378 + +ve+a+N+p+++aee+ + p+++l+ +lG +++q+++e ++++++ + G +e++ +l+ ++++g++k+ l+ lcl|FitnessBrowser__Phaeo:GFF3560 307 DGAVENALNMPSMTAEEARVMGPWVALSGHLGGFIGQMTDEPIQAINILYDGVASEMNLAALNCSVVAGIMKK-LN 381 **********************************************************************986.78 PP TIGR01327 379 eevnlvnAkavakergitveeskeeesedyknllevkveadkgevsvagtvleekepriveidgfevdlepegill 454 +vn+v+A++va+ergi+++ +++++s +++ +++v+v ++k e+svagtv+++ +pr ++i+g+++d e ++l lcl|FitnessBrowser__Phaeo:GFF3560 382 PDVNMVSAPVVARERGIQISTTNQDKSGTFDGYIKVTVVTSKRERSVAGTVFSDGKPRFIQIKGINIDAEVGAHML 457 8*************************************************************************** PP TIGR01327 455 iiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseevleeikevpeiksvk 521 +++n+D+pG+ig +g++lg++g+Nia+++lgr+e+ggea++ll +De+v++ ++++e + +++k lcl|FitnessBrowser__Phaeo:GFF3560 458 YTTNEDVPGIIGTLGQILGDMGVNIANFTLGRSEAGGEAIALLYVDEPVPAAARAALAETEFFNQIK 524 ****************************************************999999988777776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (525 nodes) Target sequences: 1 (531 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 10.42 // [ok]
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