Align phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized)
to candidate WP_011159842.1 TX73_RS21970 phosphoglycerate dehydrogenase
Query= CharProtDB::CH_004924 (525 letters) >NCBI__GCF_000195775.1:WP_011159842.1 Length = 529 Score = 421 bits (1082), Expect = e-122 Identities = 218/524 (41%), Positives = 330/524 (62%), Gaps = 5/524 (0%) Query: 3 RVLVSDKMSNDGLQPLIESDFIEIVQKNVADAEDELH----TFDALLVRSATKVTEDLFN 58 +VL+SD +S +Q + Q N+ +D+L +D L +RSATK T + Sbjct: 5 KVLISDALSEAAVQIFKDRGIDVDFQPNLGKDKDKLAEIIGNYDGLAIRSATKATAKILE 64 Query: 59 KMTSLKIVGRAGVGVDNIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQAN 118 K LK++GRAG+GVDN++I AT G+IV+N P GN+I+TAEH M+ SL R IP A+ Sbjct: 65 KANRLKVIGRAGIGVDNVEIPAATAKGIIVMNTPFGNSITTAEHAITMMLSLAREIPAAD 124 Query: 119 ISVKSREWNRTAYVGSELYGKTLGIVGLGRIGSEIAQRRGAFGMTVHVFDPFLTEERAKK 178 S ++ +W + ++G E+ KTLG++G G IGS +A R M V FDPFL+ ERAK Sbjct: 125 ASTQAGKWEKNRFMGVEITAKTLGVIGCGNIGSIVADRALGLKMKVIAFDPFLSPERAKD 184 Query: 179 IGVNSRTFEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEAAL 238 +GV E++ + AD IT+HTPLT +TK +++ IAK KKGVR+INCARGG++DE AL Sbjct: 185 LGVEKVELEDIFKRADFITLHTPLTDKTKNIIDAAAIAKMKKGVRIINCARGGLVDENAL 244 Query: 239 LEALENGHVAGAALDVFEVEPPVDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSEEVLQ 298 EAL++GHVAGAA DVF EP N L P VI TPHLGAST EAQ NVA QV+E++ Sbjct: 245 AEALKSGHVAGAAFDVFSEEPATKNVLFGLPNVICTPHLGASTTEAQENVALQVAEQMSD 304 Query: 299 FAKGLPVMSAINLPAMTKDEFAKIKPYHQIAGKIGSLVSQCMKEPVQDVAIQYEGTIAKL 358 + + +AIN P++T +E K+KP+ ++A K+GS Q + + V I YEG +A++ Sbjct: 305 YLLTGAITNAINFPSITAEEAPKLKPFIELAEKLGSFAGQLTETGITKVTITYEGEVAEM 364 Query: 359 ETSFITKALLSGFLKPRVDSTVNEVNAGGVAKERGISFSEKISSSESGYDNCISVKVTGD 418 + +T A+LSG L+P + +N V+A +AKERG+ E + ++ES Y++ I++ VT + Sbjct: 365 KIKALTSAVLSGLLRPML-GDINVVSAPVIAKERGMVVDEVVRAAESDYESLITLTVTTE 423 Query: 419 RSTFTVTATYIPHFGERIVEINGFNIDFYPTGHLVYIQHQDTTGVIGRVGRILGDNDINI 478 + +V+ T R+V+I G +D ++Y+ ++D G IG+ +LGD +NI Sbjct: 424 KQERSVSGTVYADGKPRLVDIKGIRVDAEFGSSMIYVTNEDKPGFIGKFASLLGDAKVNI 483 Query: 479 ATMQVGRKEKGGEAIMMLSFDRHLEDKIVKELTNVPDIVSVKLI 522 AT +GR +GG+AI +++ D ++++++ +P + VK + Sbjct: 484 ATFNLGRHTEGGDAIALVTIDGPAPTEVLEKVQALPQVKQVKAL 527 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: 627 Number of extensions: 32 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: 529 Length adjustment: 35 Effective length of query: 490 Effective length of database: 494 Effective search space: 242060 Effective search space used: 242060 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_011159842.1 TX73_RS21970 (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.29266.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-214 698.3 8.2 4e-214 698.1 8.2 1.0 1 lcl|NCBI__GCF_000195775.1:WP_011159842.1 TX73_RS21970 phosphoglycerate de Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195775.1:WP_011159842.1 TX73_RS21970 phosphoglycerate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 698.1 8.2 4e-214 4e-214 1 524 [. 5 528 .. 5 529 .] 0.99 Alignments for each domain: == domain 1 score: 698.1 bits; conditional E-value: 4e-214 TIGR01327 1 kvlvadklseegiellkekelevdvktgl..skeellekikdydalivRSatkvteelleaaekLkvig 67 kvl++d lse++++++k+++++vd + +l +k++l e+i +yd+l +RSatk t+++le+a++Lkvig lcl|NCBI__GCF_000195775.1:WP_011159842.1 5 KVLISDALSEAAVQIFKDRGIDVDFQPNLgkDKDKLAEIIGNYDGLAIRSATKATAKILEKANRLKVIG 73 7*************************99833567899******************************** PP TIGR01327 68 RaGvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtEl 136 RaG+GvDN++i+aat+kGi+v+N+P gn+i++aE+a++++l+laR+ip+ad+s++++kWe+++f+G+E+ lcl|NCBI__GCF_000195775.1:WP_011159842.1 74 RAGIGVDNVEIPAATAKGIIVMNTPFGNSITTAEHAITMMLSLAREIPAADASTQAGKWEKNRFMGVEI 142 ********************************************************************* PP TIGR01327 137 ygktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltk 205 ++ktlGviG G+iGs+va+ra +l+mkv+a+DP++s+e+a++lgve+++ l++++++aD+it+H+Plt+ lcl|NCBI__GCF_000195775.1:WP_011159842.1 143 TAKTLGVIGCGNIGSIVADRALGLKMKVIAFDPFLSPERAKDLGVEKVE-LEDIFKRADFITLHTPLTD 210 **********************************************666.******************* PP TIGR01327 206 etkgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvv 274 +tk++i++ ++akmKkgv+i+NcaRGG++dE+AL+eal++g+v++aa+Dvf++EP+t+n l+ l+nv+ lcl|NCBI__GCF_000195775.1:WP_011159842.1 211 KTKNIIDAAAIAKMKKGVRIINCARGGLVDENALAEALKSGHVAGAAFDVFSEEPATKNVLFGLPNVIC 279 ********************************************************************* PP TIGR01327 275 tpHlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllke 343 tpHlgAst+Eaqenva++vae+++++l + + ++a+N p+++aee+ klkp+++laeklG++a+ql+++ lcl|NCBI__GCF_000195775.1:WP_011159842.1 280 TPHLGASTTEAQENVALQVAEQMSDYLLTGAITNAINFPSITAEEAPKLKPFIELAEKLGSFAGQLTET 348 ********************************************************************* PP TIGR01327 344 avkkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknll 412 ++kv++t+eGe+ae++ ++ltsa+l+gll+++l ++n+v+A+++akerg+ v e +++++dy++l+ lcl|NCBI__GCF_000195775.1:WP_011159842.1 349 GITKVTITYEGEVAEMKIKALTSAVLSGLLRPMLG-DINVVSAPVIAKERGMVVDEVVRAAESDYESLI 416 **********************************9.8******************************** PP TIGR01327 413 evkveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNias 481 +++v+++k+e+sv+gtv+++ +pr+v+i+g++vd e+ +++++n+DkpG+igk +sllg+a +Nia+ lcl|NCBI__GCF_000195775.1:WP_011159842.1 417 TLTVTTEKQERSVSGTVYADGKPRLVDIKGIRVDAEFGSSMIYVTNEDKPGFIGKFASLLGDAKVNIAT 485 ********************************************************************* PP TIGR01327 482 mqlgrkekggealmllslDeevseevleeikevpeiksvklve 524 ++lgr+++gg+a++l+++D +++ evle+++++p++k+vk+++ lcl|NCBI__GCF_000195775.1:WP_011159842.1 486 FNLGRHTEGGDAIALVTIDGPAPTEVLEKVQALPQVKQVKALT 528 ***************************************9875 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 10.50 // [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