Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_011779357.1 MVAN_RS10670 phosphoglycerate dehydrogenase
Query= BRENDA::P9WNX3 (528 letters) >NCBI__GCF_000015305.1:WP_011779357.1 Length = 528 Score = 846 bits (2185), Expect = 0.0 Identities = 446/528 (84%), Positives = 482/528 (91%) Query: 1 MSLPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVL 60 MSLPVVLIADKLA STV ALGDQVEVRWVDGPDR+KLLAAV +ADALLVRSATTVDAEVL Sbjct: 1 MSLPVVLIADKLAQSTVEALGDQVEVRWVDGPDREKLLAAVADADALLVRSATTVDAEVL 60 Query: 61 AAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAA 120 AAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAA+RQIPAA Sbjct: 61 AAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAAARQIPAA 120 Query: 121 DASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAA 180 DA+LREH+WKRSSFSGTEIFGKTVGVVGLGRIGQLVAQR+AAFGA++ AYDPYVS ARAA Sbjct: 121 DATLREHSWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRLAAFGAHITAYDPYVSHARAA 180 Query: 181 QLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAA 240 QLGIELL+LD+LL RADFISVHLPKT ETAGLI KEALAKTKPGVIIVNAARGGL+DEAA Sbjct: 181 QLGIELLTLDELLGRADFISVHLPKTKETAGLIGKEALAKTKPGVIIVNAARGGLIDEAA 240 Query: 241 LADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVR 300 LADAI GHVR AGLDVF+TEPCTDSPLFEL QVVVTPHLGAST EAQDRAGTDVA SV+ Sbjct: 241 LADAINSGHVRGAGLDVFSTEPCTDSPLFELPQVVVTPHLGASTVEAQDRAGTDVAASVK 300 Query: 301 LALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEE 360 LALAGEFVPDAVNVGGG V EEVAPWLDLVRKLG+L GVLS E PVSL VQV+GELA+EE Sbjct: 301 LALAGEFVPDAVNVGGGAVGEEVAPWLDLVRKLGLLVGVLSSEPPVSLQVQVQGELASEE 360 Query: 361 VEVLRLSALRGLFSAVIEDAVTFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGAD 420 VEVL+LSALRGLFSAVIE VTFVNAPALA+ERGV A I A+ES NHRSVVDVRAV AD Sbjct: 361 VEVLKLSALRGLFSAVIEHPVTFVNAPALASERGVEASITTATESANHRSVVDVRAVAAD 420 Query: 421 GSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKIGTLLGTAGVN 480 GS V V+GTL GPQL +KIVQINGR+ +LRA+G+NLII+Y D+PGALGKIGTLLG A VN Sbjct: 421 GSTVNVAGTLTGPQLVEKIVQINGRNLELRAEGVNLIINYDDQPGALGKIGTLLGGAAVN 480 Query: 481 IQAAQLSEDAEGPGATILLRLDQDVPDDVRTAIAAAVDAYKLEVVDLS 528 I AAQLS+DA+G GAT++LRLD++VP +V AI V+A LEVVDL+ Sbjct: 481 ILAAQLSQDADGIGATVMLRLDREVPGEVLAAIGRDVNAVTLEVVDLT 528 Lambda K H 0.317 0.133 0.370 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: 857 Number of extensions: 23 Number of successful extensions: 1 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: 528 Length of database: 528 Length adjustment: 35 Effective length of query: 493 Effective length of database: 493 Effective search space: 243049 Effective search space used: 243049 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_011779357.1 MVAN_RS10670 (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.9855.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-200 651.4 6.7 6.5e-200 651.2 6.7 1.0 1 lcl|NCBI__GCF_000015305.1:WP_011779357.1 MVAN_RS10670 phosphoglycerate de Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015305.1:WP_011779357.1 MVAN_RS10670 phosphoglycerate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 651.2 6.7 6.5e-200 6.5e-200 2 524 .. 6 526 .. 5 527 .. 0.97 Alignments for each domain: == domain 1 score: 651.2 bits; conditional E-value: 6.5e-200 TIGR01327 2 vlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaG 70 vl+adkl+++++e+l ++ +ev++ +g ++e+ll+++ d+dal+vRSat+v++e+l+aa+kLk+++RaG lcl|NCBI__GCF_000015305.1:WP_011779357.1 6 VLIADKLAQSTVEALGDQ-VEVRWVDGPDREKLLAAVADADALLVRSATTVDAEVLAAAPKLKIVARAG 73 9**************977.8************************************************* PP TIGR01327 71 vGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygk 139 vG+DN+d++aat++G+lvvNaP++n++saaE+alallla+aR+ip+ad+ ++e+ W+r++f+GtE++gk lcl|NCBI__GCF_000015305.1:WP_011779357.1 74 VGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAAARQIPAADATLREHSWKRSSFSGTEIFGK 142 ********************************************************************* PP TIGR01327 140 tlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketk 208 t+Gv+GlGriG+ va+r +a+g+++ ayDPy+s+++a++lg+el +ldell +aD+i+vH+P+tket+ lcl|NCBI__GCF_000015305.1:WP_011779357.1 143 TVGVVGLGRIGQLVAQRLAAFGAHITAYDPYVSHARAAQLGIEL-LTLDELLGRADFISVHLPKTKETA 210 *******************************************5.55********************** PP TIGR01327 209 gligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpH 277 gligke+lak+K+gviivN+aRGG+idE+AL++a+++g+vr+a+lDvf++EP+td++l+el++vvvtpH lcl|NCBI__GCF_000015305.1:WP_011779357.1 211 GLIGKEALAKTKPGVIIVNAARGGLIDEAALADAINSGHVRGAGLDVFSTEPCTDSPLFELPQVVVTPH 279 ********************************************************************* PP TIGR01327 278 lgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavk 346 lgAst Eaq++++++va +v+ al+ge+v++avN++ + e+++p+ldl++klG l+++l++e + lcl|NCBI__GCF_000015305.1:WP_011779357.1 280 LGASTVEAQDRAGTDVAASVKLALAGEFVPDAVNVGG--GAVGEEVAPWLDLVRKLGLLVGVLSSEPPV 346 ************************************9..677889************************ PP TIGR01327 347 kvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknllevk 415 +++v+++Gela+ee+e+l+ ++l+gl+++v+e+ v++vnA+a+a erg++ +++++ es +++++++v+ lcl|NCBI__GCF_000015305.1:WP_011779357.1 347 SLQVQVQGELASEEVEVLKLSALRGLFSAVIEHPVTFVNAPALASERGVEASITTATESANHRSVVDVR 415 ********************************************************************9 PP TIGR01327 416 veadkg.evsvagtvlee.kepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasm 482 + a++g +v+vagt+ + ++iv+i+g +++l++eg++lii++ D+pG++gk+g+llg a +Ni ++ lcl|NCBI__GCF_000015305.1:WP_011779357.1 416 AVAADGsTVNVAGTLTGPqLVEKIVQINGRNLELRAEGVNLIINYDDQPGALGKIGTLLGGAAVNILAA 484 887776599*******984689*********************************************** PP TIGR01327 483 qlgrkekggealmllslDeevseevleeikevpeiksvklve 524 ql++++ g a+++l+lD+ev+ evl++i ++ ++++v+ lcl|NCBI__GCF_000015305.1:WP_011779357.1 485 QLSQDADGIGATVMLRLDREVPGEVLAAIGRDVNAVTLEVVD 526 *****************************8877777777776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (525 nodes) Target sequences: 1 (528 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: 8.09 // [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