Align phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized)
to candidate WP_012113222.1 XAUT_RS06030 phosphoglycerate dehydrogenase
Query= CharProtDB::CH_004924 (525 letters) >NCBI__GCF_000017645.1:WP_012113222.1 Length = 528 Score = 419 bits (1077), Expect = e-121 Identities = 225/524 (42%), Positives = 326/524 (62%), Gaps = 5/524 (0%) Query: 3 RVLVSDKMSNDGLQPL----IESDFIEIVQKNVADAEDELHTFDALLVRSATKVTEDLFN 58 RVL+SDK+S +Q IE DF + K+ + + +D L +RSATKVT + Sbjct: 4 RVLISDKLSPAAVQIFKDRGIEVDFQPDLGKDKDKLAEIIGNYDGLAIRSATKVTPKILQ 63 Query: 59 KMTSLKIVGRAGVGVDNIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQAN 118 K LK++GRAG+GVDN+D+ AT GVIV+N P GN+I+TAEH AM+ +L R IP A+ Sbjct: 64 KAGRLKVIGRAGIGVDNVDLPAATAKGVIVMNTPFGNSITTAEHAIAMMFALAREIPAAD 123 Query: 119 ISVKSREWNRTAYVGSELYGKTLGIVGLGRIGSEIAQRRGAFGMTVHVFDPFLTEERAKK 178 S ++ +W + ++G E+ KTLGI+G G IGS +A+R M V FDPFL+ ERA Sbjct: 124 ASTQAGKWEKNRFMGVEVTAKTLGIIGCGNIGSIVAERGVGLKMKVIAFDPFLSVERALD 183 Query: 179 IGVNSRTFEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEAAL 238 +GV +++L AD IT+HTPLT++TK +L+ E IA+TKKGVR+INCARGG++DEAAL Sbjct: 184 LGVEKVELDDLLARADFITLHTPLTEKTKNILSAENIARTKKGVRIINCARGGLVDEAAL 243 Query: 239 LEALENGHVAGAALDVFEVEPPVDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSEEVLQ 298 AL++ HVAGAA DVF VEP N L HP V+ TPHLGA+T EAQ NVA QV+E++ Sbjct: 244 RAALDSKHVAGAAFDVFAVEPAEQNPLFGHPNVVCTPHLGAATNEAQENVALQVAEQMSD 303 Query: 299 FAKGLPVMSAINLPAMTKDEFAKIKPYHQIAGKIGSLVSQCMKEPVQDVAIQYEGTIAKL 358 + + +A+N ++T +E K+KP+ +A K+GS Q ++ V I YEG +A Sbjct: 304 YLLTGAITNAVNFTSITAEEAPKLKPFIALAEKLGSFAGQLTDTDIKTVHIVYEGAVADQ 363 Query: 359 ETSFITKALLSGFLKPRVDSTVNEVNAGGVAKERGISFSEKISSSESGYDNCISVKVTGD 418 + +T A ++G L+P + S VN V+A VAKERGI E ++ YD+ IS+ V D Sbjct: 364 KVKALTSAAVAGLLRPML-SEVNVVSAPTVAKERGIVIEETTRAATGDYDSLISITVVTD 422 Query: 419 RSTFTVTATYIPHFGERIVEINGFNIDFYPTGHLVYIQHQDTTGVIGRVGRILGDNDINI 478 ++ T RIV I G N+D ++Y+ ++D G IGR +LGD +NI Sbjct: 423 TYERAISGTVFADGRPRIVNIKGINVDAEFAPSMIYVTNEDKPGFIGRFAGLLGDAGLNI 482 Query: 479 ATMQVGRKEKGGEAIMMLSFDRHLEDKIVKELTNVPDIVSVKLI 522 AT +GR GG+AI +++ D + ++ ++ +P + + K + Sbjct: 483 ATFALGRDHLGGDAIALVAVDGTVPADVLGKVQALPQVKAAKAL 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: 639 Number of extensions: 23 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: 528 Length adjustment: 35 Effective length of query: 490 Effective length of database: 493 Effective search space: 241570 Effective search space used: 241570 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_012113222.1 XAUT_RS06030 (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.21029.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.5e-209 680.7 5.7 8.4e-209 680.6 5.7 1.0 1 lcl|NCBI__GCF_000017645.1:WP_012113222.1 XAUT_RS06030 phosphoglycerate de Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000017645.1:WP_012113222.1 XAUT_RS06030 phosphoglycerate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 680.6 5.7 8.4e-209 8.4e-209 1 523 [. 4 526 .. 4 528 .] 0.99 Alignments for each domain: == domain 1 score: 680.6 bits; conditional E-value: 8.4e-209 TIGR01327 1 kvlvadklseegiellkekelevdvktgl..skeellekikdydalivRSatkvteelleaaekLkvig 67 +vl++dkls+++++++k++++evd + +l +k++l e+i +yd+l +RSatkvt ++l++a +Lkvig lcl|NCBI__GCF_000017645.1:WP_012113222.1 4 RVLISDKLSPAAVQIFKDRGIEVDFQPDLgkDKDKLAEIIGNYDGLAIRSATKVTPKILQKAGRLKVIG 72 79************************99833567899******************************** PP TIGR01327 68 RaGvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtEl 136 RaG+GvDN+d++aat+kG++v+N+P gn+i++aE+a+a+++alaR+ip+ad+s++++kWe+++f+G+E+ lcl|NCBI__GCF_000017645.1:WP_012113222.1 73 RAGIGVDNVDLPAATAKGVIVMNTPFGNSITTAEHAIAMMFALAREIPAADASTQAGKWEKNRFMGVEV 141 ********************************************************************* PP TIGR01327 137 ygktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltk 205 ++ktlG+iG G+iGs+va+r +l+mkv+a+DP++s e+a +lgve+++ ld+lla+aD+it+H+Plt+ lcl|NCBI__GCF_000017645.1:WP_012113222.1 142 TAKTLGIIGCGNIGSIVAERGVGLKMKVIAFDPFLSVERALDLGVEKVE-LDDLLARADFITLHTPLTE 209 **********************************************666.******************* PP TIGR01327 206 etkgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvv 274 +tk+++++e++a++Kkgv+i+NcaRGG++dE+AL al++++v++aa+Dvf+ EP+++n+l+ ++nvv lcl|NCBI__GCF_000017645.1:WP_012113222.1 210 KTKNILSAENIARTKKGVRIINCARGGLVDEAALRAALDSKHVAGAAFDVFAVEPAEQNPLFGHPNVVC 278 ********************************************************************* PP TIGR01327 275 tpHlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllke 343 tpHlgA t+Eaqenva++vae+++++l + + ++avN +++aee+ klkp+++laeklG++a+ql+++ lcl|NCBI__GCF_000017645.1:WP_012113222.1 279 TPHLGAATNEAQENVALQVAEQMSDYLLTGAITNAVNFTSITAEEAPKLKPFIALAEKLGSFAGQLTDT 347 ********************************************************************* PP TIGR01327 344 avkkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknll 412 +k+v++ +eG +a++++++ltsa+++gll+++l+ evn+v+A++vakergi +ee++++++ dy++l+ lcl|NCBI__GCF_000017645.1:WP_012113222.1 348 DIKTVHIVYEGAVADQKVKALTSAAVAGLLRPMLS-EVNVVSAPTVAKERGIVIEETTRAATGDYDSLI 415 **********************************9.9******************************** PP TIGR01327 413 evkveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNias 481 +++v +d+ e++++gtv+++ priv+i+g++vd e+ +++++n+DkpG+ig+ + llg+ag+Nia+ lcl|NCBI__GCF_000017645.1:WP_012113222.1 416 SITVVTDTYERAISGTVFADGRPRIVNIKGINVDAEFAPSMIYVTNEDKPGFIGRFAGLLGDAGLNIAT 484 ********************************************************************* PP TIGR01327 482 mqlgrkekggealmllslDeevseevleeikevpeiksvklv 523 ++lgr++ gg+a++l+ +D +v+++vl +++++p++k +k++ lcl|NCBI__GCF_000017645.1:WP_012113222.1 485 FALGRDHLGGDAIALVAVDGTVPADVLGKVQALPQVKAAKAL 526 ************************************999876 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 10.78 // [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