Align phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized)
to candidate SMc00641 SMc00641 D-3-phosphoglycerate dehydrogenase
Query= CharProtDB::CH_004924 (525 letters) >FitnessBrowser__Smeli:SMc00641 Length = 531 Score = 411 bits (1056), Expect = e-119 Identities = 217/514 (42%), Positives = 332/514 (64%), Gaps = 9/514 (1%) Query: 3 RVLVSDKMSNDGLQPL----IESDFIEIVQKNVADAEDELHTFDALLVRSATKVTEDLFN 58 RVLVSD++S +Q +E DF + K+ + + +D L +RSATKVTE L Sbjct: 4 RVLVSDELSETAVQIFRDHGVEVDFQPKLGKDKEKLAEIIGNYDGLAIRSATKVTEKLIA 63 Query: 59 KMTSLKIVGRAGVGVDNIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQAN 118 T+LK+VGRAG+GVDN+DI A++ G+IV+N P GN+I+TAEH A++ ++ R +P A+ Sbjct: 64 AATNLKVVGRAGIGVDNVDIPAASRRGIIVMNTPFGNSITTAEHAIALMFAVARQLPAAD 123 Query: 119 ISVKSREWNRTAYVGSELYGKTLGIVGLGRIGSEIAQRRGAFGMTVHV--FDPFLTEERA 176 S ++ +W ++ ++G E+ GK LG++G G IGS + R A G+ +HV +DPFL++ERA Sbjct: 124 GSTQAGKWEKSKFMGVEITGKVLGVIGAGNIGSIVCAR--AIGLKMHVIAYDPFLSKERA 181 Query: 177 KKIGVNSRTFEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEA 236 +++GV +E+L AD I++H PLT +T+ +LN E IAK K GVR+INCARGG++DE Sbjct: 182 EEMGVVKVELDELLAQADFISLHVPLTDKTRNILNAEAIAKAKPGVRIINCARGGLVDEK 241 Query: 237 ALLEALENGHVAGAALDVFEVEPPVDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSEEV 296 AL EAL+ GHVAGA DVFEVEP ++ L P V+ TPHLGAST EAQ NVA QV+E++ Sbjct: 242 ALAEALKAGHVAGAGFDVFEVEPATESPLFGLPNVVCTPHLGASTTEAQENVALQVAEQM 301 Query: 297 LQFAKGLPVMSAINLPAMTKDEFAKIKPYHQIAGKIGSLVSQCMKEPVQDVAIQYEGTIA 356 ++ V +AIN+P++T +E +KP+ ++A +G+ V Q + ++++ I Y+G+ A Sbjct: 302 SEYLVKGAVTNAINMPSITAEEAPILKPFIRLADVLGAFVGQVTESAIKEIEILYDGSTA 361 Query: 357 KLETSFITKALLSGFLKPRVDSTVNEVNAGGVAKERGISFSEKISSSESGYDNCISVKVT 416 + T +T A L+G ++P+V + VN V+A + KE+G+ SE +D I + V Sbjct: 362 AMNTKALTSAALAGLIRPQV-ADVNMVSAPVMVKEKGVILSEVKRDKTGVFDGYIKLTVK 420 Query: 417 GDRSTFTVTATYIPHFGERIVEINGFNIDFYPTGHLVYIQHQDTTGVIGRVGRILGDNDI 476 T +V T R ++I G N+D H+VYI + D G+IG +G LGD + Sbjct: 421 TANQTRSVAGTVFSDGKPRFIQIKGINLDADVGNHMVYITNTDVPGMIGFIGSTLGDAGV 480 Query: 477 NIATMQVGRKEKGGEAIMMLSFDRHLEDKIVKEL 510 NIA Q+GR+++GG+AI +L D + + ++ +L Sbjct: 481 NIANFQLGREKQGGDAIALLYVDGPVSEIVLDKL 514 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: 631 Number of extensions: 26 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 SMc00641 SMc00641 (D-3-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.5134.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-206 671.9 9.0 4.2e-206 671.7 9.0 1.0 1 lcl|FitnessBrowser__Smeli:SMc00641 SMc00641 D-3-phosphoglycerate de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc00641 SMc00641 D-3-phosphoglycerate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 671.7 9.0 4.2e-206 4.2e-206 1 521 [. 4 524 .. 4 528 .. 0.98 Alignments for each domain: == domain 1 score: 671.7 bits; conditional E-value: 4.2e-206 TIGR01327 1 kvlvadklseegiellkekelevdvktgl..skeellekikdydalivRSatkvteelleaaekLkvigRaGvGv 73 +vlv+d+lse+++++++++++evd + +l +ke+l e+i +yd+l +RSatkvte+l++aa++Lkv+gRaG+Gv lcl|FitnessBrowser__Smeli:SMc00641 4 RVLVSDELSETAVQIFRDHGVEVDFQPKLgkDKEKLAEIIGNYDGLAIRSATKVTEKLIAAATNLKVVGRAGIGV 78 79***********************998733678899************************************** PP TIGR01327 74 DNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygktlGviGlGr 148 DN+di+aa+++Gi+v+N+P gn+i++aE+a+al++a+aR++p+ad s++++kWe++kf+G+E++gk lGviG+G+ lcl|FitnessBrowser__Smeli:SMc00641 79 DNVDIPAASRRGIIVMNTPFGNSITTAEHAIALMFAVARQLPAADGSTQAGKWEKSKFMGVEITGKVLGVIGAGN 153 *************************************************************************** PP TIGR01327 149 iGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelakmKkgv 223 iGs+v ra +l+m+v+ayDP++s+e+ae++gv +++ ldella+aD+i++HvPlt++t++++++e++ak+K+gv lcl|FitnessBrowser__Smeli:SMc00641 154 IGSIVCARAIGLKMHVIAYDPFLSKERAEEMGVVKVE-LDELLAQADFISLHVPLTDKTRNILNAEAIAKAKPGV 227 **********************************666.************************************* PP TIGR01327 224 iivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpHlgAsteEaqenvavevaeevl 298 +i+NcaRGG++dEkAL+eal++g+v++a++Dvfe EP+t+++l+ l+nvv tpHlgAst+Eaqenva++vae+++ lcl|FitnessBrowser__Smeli:SMc00641 228 RIINCARGGLVDEKALAEALKAGHVAGAGFDVFEVEPATESPLFGLPNVVCTPHLGASTTEAQENVALQVAEQMS 302 *************************************************************************** PP TIGR01327 299 ealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeeselltsallkgll 373 e+l +v++a+N+p+++aee+ lkp+++la+ lG++++q++++a+k++e+ + G a++++++ltsa+l+gl+ lcl|FitnessBrowser__Smeli:SMc00641 303 EYLVKGAVTNAINMPSITAEEAPILKPFIRLADVLGAFVGQVTESAIKEIEILYDGSTAAMNTKALTSAALAGLI 377 *************************************************************************** PP TIGR01327 374 kevleeevnlvnAkavakergitveeskeeesedyknllevkveadkgevsvagtvleekepriveidgfevdle 448 +++++ +vn+v+A++++ke+g+ ++e k++++ ++ +++++v+++++++svagtv+++ +pr ++i+g+++d lcl|FitnessBrowser__Smeli:SMc00641 378 RPQVA-DVNMVSAPVMVKEKGVILSEVKRDKTGVFDGYIKLTVKTANQTRSVAGTVFSDGKPRFIQIKGINLDAD 451 ****9.8******************************************************************** PP TIGR01327 449 pegilliiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseevleeikevpeiksvk 521 +++++i+n+D+pG+ig +gs+lg+ag+Nia++qlgr+++gg+a++ll +D +vse vl+++++ ++i+++k lcl|FitnessBrowser__Smeli:SMc00641 452 VGNHMVYITNTDVPGMIGFIGSTLGDAGVNIANFQLGREKQGGDAIALLYVDGPVSEIVLDKLRANEAIRQAK 524 *****************************************************************99999987 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: 00:00:00.03 # Mc/sec: 7.66 // [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