Align phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized)
to candidate WP_013420530.1 RVAN_RS14855 phosphoglycerate dehydrogenase
Query= CharProtDB::CH_004924 (525 letters) >NCBI__GCF_000166055.1:WP_013420530.1 Length = 526 Score = 400 bits (1028), Expect = e-116 Identities = 214/518 (41%), Positives = 325/518 (62%), Gaps = 6/518 (1%) Query: 3 RVLVSDKMSNDGLQPLIESDFIEIVQKNVADAE---DELHTFDALLVRSATKVTEDLFNK 59 RVLV+DK+S + + ++ IE+ K D + + + +D L +RSATKVTE + Sbjct: 5 RVLVADKLSPAAAE-IFKNRGIEVDTKIGLDKDQLAEIIGNYDGLAIRSATKVTEKVLAS 63 Query: 60 MTSLKIVGRAGVGVDNIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQANI 119 LK+VGRAG+GVDN+D+ AT GVIV+N P GN+I+TAEH +++ +L R IP+A+ Sbjct: 64 AERLKVVGRAGIGVDNVDVPAATARGVIVMNTPFGNSITTAEHAISLLMALARQIPEADR 123 Query: 120 SVKSREWNRTAYVGSELYGKTLGIVGLGRIGSEIAQRRGAFGMTVHVFDPFLTEERAKKI 179 S ++ +W ++ ++G E+ KTLGI+G G IGS +A R M V FDPFLTEERA + Sbjct: 124 STQAGKWEKSKFMGVEVTSKTLGIIGCGNIGSIVADRAQGLRMKVIAFDPFLTEERALDL 183 Query: 180 GVNSRTFEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEAALL 239 GV + EE+ AD IT+HTPLT++TK ++N ++IA KKGVR+INCARGG+I E AL Sbjct: 184 GVERVSLEELFRRADFITLHTPLTEKTKNIINAQSIATMKKGVRIINCARGGLIVEQALA 243 Query: 240 EALENGHVAGAALDVFEVEPPVDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSEEVLQF 299 +A++ GHVAGAALDVFEVEP +N L VI+TPHLGAST EAQ NVA QV+E++ + Sbjct: 244 DAIKAGHVAGAALDVFEVEPAKENVLFGLANVISTPHLGASTSEAQENVALQVAEQMADY 303 Query: 300 AKGLPVMSAINLPAMTKDEFAKIKPYHQIAGKIGSLVSQCMKEPVQDVAIQYEGTIAKLE 359 + +A+N P++T +E K+KP+ ++A +GS Q + + ++Y G +A + Sbjct: 304 LLTGAISNAVNFPSITAEEAPKLKPFVKLAELLGSFAGQLTEAAPNFIRLEYAGDVADMN 363 Query: 360 TSFITKALLSGFLKPRVDSTVNEVNAGGVAKERGISFSEKISSSESGYDNCISVKVTGDR 419 T +T A +SG L+ + VN V+ VAKERGI E E Y+ I V + ++ Sbjct: 364 TRALTSAAISGVLRHFLH--VNMVSGPAVAKERGIQVEETKRGQEGAYETYIRVTLKTEK 421 Query: 420 STFTVTATYIPHFGERIVEINGFNIDFYPTGHLVYIQHQDTTGVIGRVGRILGDNDINIA 479 ++ T R+++IN +D ++++ + D G IG +G +LGD +NIA Sbjct: 422 QEISIAGTVFSDGKPRVIQINHVPMDAEFAPNMLFTVNADKPGHIGALGTLLGDEGVNIA 481 Query: 480 TMQVGRKEKGGEAIMMLSFDRHLEDKIVKELTNVPDIV 517 T +GR+ +GG+A+ +++ D + D +++ +P +V Sbjct: 482 TFNLGREAQGGKAMALVTVDEPVSDATIQKALALPHVV 519 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: 636 Number of extensions: 24 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: 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_013420530.1 RVAN_RS14855 (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.27994.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-208 679.5 7.1 1.9e-208 679.4 7.1 1.0 1 lcl|NCBI__GCF_000166055.1:WP_013420530.1 RVAN_RS14855 phosphoglycerate de Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000166055.1:WP_013420530.1 RVAN_RS14855 phosphoglycerate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 679.4 7.1 1.9e-208 1.9e-208 1 521 [. 5 522 .. 5 526 .] 0.99 Alignments for each domain: == domain 1 score: 679.4 bits; conditional E-value: 1.9e-208 TIGR01327 1 kvlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRa 69 +vlvadkls+++ e++k++++evd+k gl+k++l e+i +yd+l +RSatkvte++l+ ae+Lkv+gRa lcl|NCBI__GCF_000166055.1:WP_013420530.1 5 RVLVADKLSPAAAEIFKNRGIEVDTKIGLDKDQLAEIIGNYDGLAIRSATKVTEKVLASAERLKVVGRA 73 79******************************************************************* PP TIGR01327 70 GvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElyg 138 G+GvDN+d++aat++G++v+N+P gn+i++aE+a+ ll+alaR+ip+ad+s++++kWe++kf+G+E+++ lcl|NCBI__GCF_000166055.1:WP_013420530.1 74 GIGVDNVDVPAATARGVIVMNTPFGNSITTAEHAISLLMALARQIPEADRSTQAGKWEKSKFMGVEVTS 142 ********************************************************************* PP TIGR01327 139 ktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltket 207 ktlG+iG G+iGs+va+ra++l+mkv+a+DP+++ee+a +lgve+++ l+el+++aD+it+H+Plt++t lcl|NCBI__GCF_000166055.1:WP_013420530.1 143 KTLGIIGCGNIGSIVADRAQGLRMKVIAFDPFLTEERALDLGVERVS-LEELFRRADFITLHTPLTEKT 210 ********************************************776.********************* PP TIGR01327 208 kgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtp 276 k++i+++++a mKkgv+i+NcaRGG+i E+AL++a+++g+v++aalDvfe EP+++n l+ l+nv+ tp lcl|NCBI__GCF_000166055.1:WP_013420530.1 211 KNIINAQSIATMKKGVRIINCARGGLIVEQALADAIKAGHVAGAALDVFEVEPAKENVLFGLANVISTP 279 ********************************************************************* PP TIGR01327 277 HlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeav 345 HlgAst+Eaqenva++vae++ ++l + + ++avN p+++aee+ klkp+++lae lG++a+ql+++a+ lcl|NCBI__GCF_000166055.1:WP_013420530.1 280 HLGASTSEAQENVALQVAEQMADYLLTGAISNAVNFPSITAEEAPKLKPFVKLAELLGSFAGQLTEAAP 348 ********************************************************************* PP TIGR01327 346 kkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknllev 414 + +++++ G++a++++ +ltsa+++g+l++ l+ vn+v+ +avakergi+vee+k+ ++ y+++++v lcl|NCBI__GCF_000166055.1:WP_013420530.1 349 NFIRLEYAGDVADMNTRALTSAAISGVLRHFLH--VNMVSGPAVAKERGIQVEETKRGQEGAYETYIRV 415 *******************************98..********************************** PP TIGR01327 415 kveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmq 483 +++++k+e+s+agtv+++ +pr+++i+++ +d e+ +l++ n DkpG ig +g+llg+ g+Nia+++ lcl|NCBI__GCF_000166055.1:WP_013420530.1 416 TLKTEKQEISIAGTVFSDGKPRVIQINHVPMDAEFAPNMLFTVNADKPGHIGALGTLLGDEGVNIATFN 484 ********************************************************************* PP TIGR01327 484 lgrkekggealmllslDeevseevleeikevpeiksvk 521 lgr+++gg+a++l+++De+vs+ +++ ++p++ +++ lcl|NCBI__GCF_000166055.1:WP_013420530.1 485 LGREAQGGKAMALVTVDEPVSDATIQKALALPHVVRAA 522 ***************************99999998776 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 11.77 // [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