Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_012676553.1 PERMA_RS01650 phosphoglycerate dehydrogenase
Query= BRENDA::Q9Z564 (529 letters) >NCBI__GCF_000021565.1:WP_012676553.1 Length = 529 Score = 357 bits (916), Expect = e-103 Identities = 210/515 (40%), Positives = 303/515 (58%), Gaps = 10/515 (1%) Query: 7 VLIAEELSPATVDALGPDFEIR--HCNGADRAELLPAIADVDAILVRSATKVDAEAVAAA 64 VL+ + +S +D L D EI + +ELL I+D DAI+ RS T V E + A Sbjct: 4 VLVTDHISSVGLDILNNDEEIELDYQPEIQWSELLEIISDYDAIITRSRTPVTEELLERA 63 Query: 65 KKLKVVARAGVGLDNVDVSAATKAGVMVVNAPTSNIVTAAELACGLIVATARNIPQANAA 124 K+LKVV RAGVG+DNVD+ AA++ G++VVN P +N V AAEL + A R + A+ + Sbjct: 64 KRLKVVGRAGVGVDNVDLEAASRRGILVVNTPGANTVGAAELTIAHMYAVLRKLHLAHES 123 Query: 125 LKNGEWKRSKYTGVELAEKTLGVVGLGRIGALVAQRMSAFGMKVVAYDPYVQPARAAQMG 184 + GEW R K+ G EL K +G++GLG +G+ VA R A G KV+AYDPY+ + ++G Sbjct: 124 MLQGEWNRKKFMGEELDGKVVGIIGLGNVGSQVAIRCKAAGSKVIAYDPYIPREKGDRLG 183 Query: 185 VKVL-SLDELLEVSDFITVHLPKTPETLGLIGDEALRKVKPSVRIVNAARGGIVDEEALY 243 V+++ +L+EL+ SD +T+H P T ET G+IG + +K V +N ARGGIVDE+A+Y Sbjct: 184 VELVDTLEELIRRSDIVTLHCPLTEETRGMIGRKEFEMMKDGVYFINCARGGIVDEDAMY 243 Query: 244 SALKEGRVAGAGLDVYAKEPCTD--SPLFEFDQVVATPHLGASTDEAQEKAGIAVAKSVR 301 +K+G+ AG GLDVY KEP D +FEF + +PH+GA+T E+Q+K I +AK V Sbjct: 244 DFMKKGKFAGIGLDVYGKEPPDDRIRRIFEFPNISLSPHIGANTYESQDKVAIKIAKQVI 303 Query: 302 LALAGELVPDAVNVQGGVIA--EDVKPGLPLAERLGRIFTALAGEVAVRLDVEVYGEITQ 359 AL G+ V AVN V E++K L LAERLG T AG L VEV G I + Sbjct: 304 AALKGQFVEAAVNAPFTVTEGFENIKAYLLLAERLGSFLTQYAGGNFRELHVEVRGSIAE 363 Query: 360 HDVKVLELSALKGVFEDVVDETVSYVNAPLFAQERGVEVRLTTSSESPEHRNVVIVRGTL 419 H VK + LKG ++D V+ +NAP A+ERG+EV +T E + + + Sbjct: 364 H-VKPIVAYVLKGFLSPILDRPVNIINAPFLAKERGIEVVESTREEGLNFKEFIKITAK- 421 Query: 420 SDGEEVSVSGTLAGPKHLQKIVAIGEYDVDLALADHMVVLRYEDRPGVVGTVGRIIGEAG 479 +G+E +V GT K KI+ I Y +D+ ++V +D PGV+ +G I+ Sbjct: 422 DNGKEHTVGGTAFYGK-FPKIMLIDRYWIDIDPEGVILVFENKDVPGVIAKLGEILARHN 480 Query: 480 LNIAGMQVARATVGGEALAVLTVDDTVPSGVLAEV 514 +NIAG ++ R G AL L +D+ + +L E+ Sbjct: 481 INIAGFRLGRLEKGKIALGALQLDERINEAILEEI 515 Lambda K H 0.315 0.133 0.362 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: 677 Number of extensions: 33 Number of successful extensions: 7 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: 529 Length of database: 529 Length adjustment: 35 Effective length of query: 494 Effective length of database: 494 Effective search space: 244036 Effective search space used: 244036 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_012676553.1 PERMA_RS01650 (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.3157.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-207 674.8 0.4 5.1e-207 674.7 0.4 1.0 1 lcl|NCBI__GCF_000021565.1:WP_012676553.1 PERMA_RS01650 phosphoglycerate d Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021565.1:WP_012676553.1 PERMA_RS01650 phosphoglycerate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 674.7 0.4 5.1e-207 5.1e-207 1 523 [. 3 527 .. 3 529 .] 0.99 Alignments for each domain: == domain 1 score: 674.7 bits; conditional E-value: 5.1e-207 TIGR01327 1 kvlvadklseegie.llkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigR 68 kvlv+d++s+ g++ l +++e+e+d++ +++ elle+i dyda+i+RS+t+vteelle+a++Lkv+gR lcl|NCBI__GCF_000021565.1:WP_012676553.1 3 KVLVTDHISSVGLDiLNNDEEIELDYQPEIQWSELLEIISDYDAIITRSRTPVTEELLERAKRLKVVGR 71 7*************7778899************************************************ PP TIGR01327 69 aGvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtEly 137 aGvGvDN+d+eaa+++GilvvN+P +nt++aaEl++a++ a+ Rk++ a++s+ +++W+rkkf+G+El lcl|NCBI__GCF_000021565.1:WP_012676553.1 72 AGVGVDNVDLEAASRRGILVVNTPGANTVGAAELTIAHMYAVLRKLHLAHESMLQGEWNRKKFMGEELD 140 ********************************************************************* PP TIGR01327 138 gktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltke 206 gk +G+iGlG++Gs+va r+ka g kv+ayDPyi++ek ++lgvel+++l+el++++D++t+H Plt+e lcl|NCBI__GCF_000021565.1:WP_012676553.1 141 GKVVGIIGLGNVGSQVAIRCKAAGSKVIAYDPYIPREKGDRLGVELVDTLEELIRRSDIVTLHCPLTEE 209 ********************************************************************* PP TIGR01327 207 tkgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPpt..dnklleldnvv 273 t+g+ig++e++ mK+gv+ +NcaRGGi+dE+A+++ +++gk ++++lDv+ kEPp +++e++n++ lcl|NCBI__GCF_000021565.1:WP_012676553.1 210 TRGMIGRKEFEMMKDGVYFINCARGGIVDEDAMYDFMKKGKFAGIGLDVYGKEPPDdrIRRIFEFPNIS 278 *******************************************************944479******** PP TIGR01327 274 vtpHlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllk 342 ++pH+gA+t+E+q++va+++a++v+ alkg++ve avN+p + +e +e++k+yl lae+lG++ +q+++ lcl|NCBI__GCF_000021565.1:WP_012676553.1 279 LSPHIGANTYESQDKVAIKIAKQVIAALKGQFVEAAVNAPFTVTEGFENIKAYLLLAERLGSFLTQYAG 347 ********************************************************************* PP TIGR01327 343 eavkkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknl 411 ++ ++++v+++G +ae+ +++++ +lkg+l+++l++ vn++nA+++akergi+v es++ee ++k+ lcl|NCBI__GCF_000021565.1:WP_012676553.1 348 GNFRELHVEVRGSIAEHV-KPIVAYVLKGFLSPILDRPVNIINAPFLAKERGIEVVESTREEGLNFKEF 415 ***************986.9999********************************************** PP TIGR01327 412 levkveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNia 480 ++++++ + +e++v+gt + +k p+i+ id++ +d+ peg++l+++nkD+pGvi+k+g++l++++iNia lcl|NCBI__GCF_000021565.1:WP_012676553.1 416 IKITAKDNGKEHTVGGTAFYGKFPKIMLIDRYWIDIDPEGVILVFENKDVPGVIAKLGEILARHNINIA 484 ********************************************************************* PP TIGR01327 481 smqlgrkekggealmllslDeevseevleeikevpeiksvklv 523 +++lgr ekg+ al l+lDe+++e +leei+++pei ++k + lcl|NCBI__GCF_000021565.1:WP_012676553.1 485 GFRLGRLEKGKIALGALQLDERINEAILEEIQNIPEIIKAKEI 527 **************************************99987 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 7.49 // [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