Align phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized)
to candidate WP_028314565.1 G491_RS0110525 phosphoglycerate dehydrogenase
Query= CharProtDB::CH_004924 (525 letters) >NCBI__GCF_000429905.1:WP_028314565.1 Length = 526 Score = 434 bits (1115), Expect = e-126 Identities = 229/525 (43%), Positives = 334/525 (63%), Gaps = 3/525 (0%) Query: 3 RVLVSDKMSNDGLQPLIESDFIEI-VQKNVADAEDE--LHTFDALLVRSATKVTEDLFNK 59 +VLVSDK+ G+Q E+ IE+ V + AE + + +DA+++RSATKVTE+L + Sbjct: 2 KVLVSDKLGEAGIQLFEEAQGIEVDVNTGLEPAELKKIIGDYDAIVIRSATKVTEELLDA 61 Query: 60 MTSLKIVGRAGVGVDNIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQANI 119 +LK+VGRAG+G+DN+DI ATK GV+V+N P GN ++TAEH +M+ SL R+IP+ Sbjct: 62 APNLKVVGRAGIGLDNVDIPAATKRGVVVMNTPGGNVVTTAEHAISMMLSLTRNIPRGTA 121 Query: 120 SVKSREWNRTAYVGSELYGKTLGIVGLGRIGSEIAQRRGAFGMTVHVFDPFLTEERAKKI 179 S+K+ +W++ G E++ KTLG++G G IGS A R M V V DP +T ER +K Sbjct: 122 SLKAGKWDKKLLQGKEIFNKTLGVIGFGNIGSIAADRARGLRMNVIVADPHVTPERIEKA 181 Query: 180 GVNSRTFEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEAALL 239 G + + +E+ E +D ITVH P KET GLLNK+ AK KKGV +INCARGGI+DEA L Sbjct: 182 GFEAVSLDELYERSDYITVHVPKMKETIGLLNKDAFAKMKKGVMVINCARGGIVDEADLY 241 Query: 240 EALENGHVAGAALDVFEVEPPVDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSEEVLQF 299 +A++ G VAGAALDVF EPP L + VI TPHLGAST EAQ NVA V+E+++ + Sbjct: 242 DAIQEGKVAGAALDVFATEPPGVIPLFELDNVICTPHLGASTAEAQTNVAVAVAEQIIAY 301 Query: 300 AKGLPVMSAINLPAMTKDEFAKIKPYHQIAGKIGSLVSQCMKEPVQDVAIQYEGTIAKLE 359 + V++A+N P++T D K+KP + ++G L +Q + PV+ ++I+Y G L+ Sbjct: 302 LQTGTVINAVNAPSVTGDLLEKLKPLLTLGDRMGCLQAQLAQGPVKSISIEYYGDFRGLD 361 Query: 360 TSFITKALLSGFLKPRVDSTVNEVNAGGVAKERGISFSEKISSSESGYDNCISVKVTGDR 419 S +T A+L GFL P + VN VNAG +A+ERG+S +E + ++N I V D Sbjct: 362 LSPVTTAILKGFLTPALKDDVNFVNAGMLAQERGVSVTETTQADSKDFNNLIKVIAKSDA 421 Query: 420 STFTVTATYIPHFGERIVEINGFNIDFYPTGHLVYIQHQDTTGVIGRVGRILGDNDINIA 479 +T TV+ T +IV I+ F ++ P GH++ I + D G IG VG +LG+ +NIA Sbjct: 422 ATHTVSGTIYGKAEPKIVRIDSFRVEMVPEGHVLLIHNIDKPGAIGSVGSMLGEASVNIA 481 Query: 480 TMQVGRKEKGGEAIMMLSFDRHLEDKIVKELTNVPDIVSVKLIDL 524 MQVG++E G +++ D D +V +L +P + SV ++L Sbjct: 482 RMQVGQEEDGNRNFIVMETDTETPDDVVAKLRELPLVKSVITVEL 526 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: 665 Number of extensions: 26 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: 525 Length of database: 526 Length adjustment: 35 Effective length of query: 490 Effective length of database: 491 Effective search space: 240590 Effective search space used: 240590 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 WP_028314565.1 G491_RS0110525 (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.28185.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-202 658.6 7.9 4.3e-202 658.4 7.9 1.0 1 lcl|NCBI__GCF_000429905.1:WP_028314565.1 G491_RS0110525 phosphoglycerate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429905.1:WP_028314565.1 G491_RS0110525 phosphoglycerate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 658.4 7.9 4.3e-202 4.3e-202 1 525 [] 2 526 .] 2 526 .] 0.99 Alignments for each domain: == domain 1 score: 658.4 bits; conditional E-value: 4.3e-202 TIGR01327 1 kvlvadklseegie.llkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigR 68 kvlv+dkl e+gi+ +++ +++evdv+tgl+ +el ++i dyda+++RSatkvteell+aa++Lkv+gR lcl|NCBI__GCF_000429905.1:WP_028314565.1 2 KVLVSDKLGEAGIQlFEEAQGIEVDVNTGLEPAELKKIIGDYDAIVIRSATKVTEELLDAAPNLKVVGR 70 7*************7778899************************************************ PP TIGR01327 69 aGvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtEly 137 aG+G+DN+di+aatk+G++v+N+P gn +++aE+a+ ++l+l+R+ip+ ++s+k++kW++k G E++ lcl|NCBI__GCF_000429905.1:WP_028314565.1 71 AGIGLDNVDIPAATKRGVVVMNTPGGNVVTTAEHAISMMLSLTRNIPRGTASLKAGKWDKKLLQGKEIF 139 ********************************************************************* PP TIGR01327 138 gktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltke 206 +ktlGviG+G+iGs+ a+ra++l+m+v++ DP++++e+ ek g e + +ldel +++D itvHvP+ ke lcl|NCBI__GCF_000429905.1:WP_028314565.1 140 NKTLGVIGFGNIGSIAADRARGLRMNVIVADPHVTPERIEKAGFE-AVSLDELYERSDYITVHVPKMKE 207 *********************************************.666******************** PP TIGR01327 207 tkgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvt 275 t+gl++k+++akmKkgv+++NcaRGGi+dE+ L++a++egkv++aalDvf++EPp +l+eldnv+ t lcl|NCBI__GCF_000429905.1:WP_028314565.1 208 TIGLLNKDAFAKMKKGVMVINCARGGIVDEADLYDAIQEGKVAGAALDVFATEPPGVIPLFELDNVICT 276 ********************************************************************* PP TIGR01327 276 pHlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkea 344 pHlgAst+Eaq+nvav vae+++ +l++ +v +avN+p+++ + leklkp l+l++++G l ql+++ lcl|NCBI__GCF_000429905.1:WP_028314565.1 277 PHLGASTAEAQTNVAVAVAEQIIAYLQTGTVINAVNAPSVTGDLLEKLKPLLTLGDRMGCLQAQLAQGP 345 ********************************************************************* PP TIGR01327 345 vkkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknlle 413 vk++++++ G++ + +++t+a+lkg+l ++l+++vn+vnA ++a+erg++v+e+++++s+d++nl++ lcl|NCBI__GCF_000429905.1:WP_028314565.1 346 VKSISIEYYGDFRGLDLSPVTTAILKGFLTPALKDDVNFVNAGMLAQERGVSVTETTQADSKDFNNLIK 414 ********************************************************************* PP TIGR01327 414 vkveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasm 482 v +++d +++v+gt++++ ep+iv+id+f+v++ peg++l+i+n DkpG+ig+vgs+lgea +Nia m lcl|NCBI__GCF_000429905.1:WP_028314565.1 415 VIAKSDAATHTVSGTIYGKAEPKIVRIDSFRVEMVPEGHVLLIHNIDKPGAIGSVGSMLGEASVNIARM 483 ********************************************************************* PP TIGR01327 483 qlgrkekggealmllslDeevseevleeikevpeiksvklvel 525 q+g++e g+ ++++ D e +++v+++++e+p +ksv +vel lcl|NCBI__GCF_000429905.1:WP_028314565.1 484 QVGQEEDGNRNFIVMETDTETPDDVVAKLRELPLVKSVITVEL 526 ***************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (525 nodes) Target sequences: 1 (526 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: 9.95 // [ok]
This GapMind analysis is from Apr 10 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