Align phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized)
to candidate WP_012758842.1 RLEG_RS17215 phosphoglycerate dehydrogenase
Query= CharProtDB::CH_004924 (525 letters) >NCBI__GCF_000023185.1:WP_012758842.1 Length = 531 Score = 432 bits (1111), Expect = e-125 Identities = 225/515 (43%), Positives = 340/515 (66%), Gaps = 9/515 (1%) Query: 3 RVLVSDKMSNDGLQPL----IESDFIEIVQKNVADAEDELHTFDALLVRSATKVTEDLFN 58 RVLVSD++S +Q +E DF + K+ + + +D L +RSATKVTE + Sbjct: 4 RVLVSDELSETAVQIFRDRGVEVDFEPQLGKDKDRLLEVIGKYDGLAIRSATKVTEKIIE 63 Query: 59 KMTSLKIVGRAGVGVDNIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQAN 118 T+LK+VGRAG+GVDN+DI A++ G+IV+N P GN+I+TAEH A++ ++ R +P A+ Sbjct: 64 GATNLKVVGRAGIGVDNVDIPAASRRGIIVMNTPFGNSITTAEHAIALMFAVARQLPAAD 123 Query: 119 ISVKSREWNRTAYVGSELYGKTLGIVGLGRIGSEIAQRRGAFGMTVHV--FDPFLTEERA 176 S ++ +W ++ ++G E+ GKTLG++G G IGS + R A G+ +HV +DPFL++ERA Sbjct: 124 TSTQAGKWEKSKFMGVEITGKTLGVIGAGNIGSIVCAR--AIGLKMHVVAYDPFLSKERA 181 Query: 177 KKIGVNSRTFEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEA 236 +++GV EE+ AD IT+H P+T +T+G+LNKE +AKTK GVR+INCARGG++DEA Sbjct: 182 EEMGVTKVELEELFARADFITLHVPMTDKTRGILNKEALAKTKPGVRIINCARGGLVDEA 241 Query: 237 ALLEALENGHVAGAALDVFEVEPPVDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSEEV 296 AL EA+++GHVAGAA DVFEVEP ++ L P V+ TPHLGAST EAQ NVA QV+E++ Sbjct: 242 ALAEAIKSGHVAGAAFDVFEVEPAKESPLFGLPNVVCTPHLGASTTEAQENVALQVAEQM 301 Query: 297 LQFAKGLPVMSAINLPAMTKDEFAKIKPYHQIAGKIGSLVSQCMKEPVQDVAIQYEGTIA 356 + V +AIN+P++T +E +KP+ ++A +G+ V Q +EP++++ I Y+G A Sbjct: 302 ADYLVNGAVSNAINMPSITAEEAPILKPFIRLADVLGAFVGQVTEEPIKEIEILYDGITA 361 Query: 357 KLETSFITKALLSGFLKPRVDSTVNEVNAGGVAKERGISFSEKISSSESGYDNCISVKVT 416 + T +T A L+G ++P+V + VN V+A + KE+GI SE +D I + VT Sbjct: 362 NMNTRALTSAALAGLIRPQV-ADVNMVSAPIMIKEKGIVLSEVKRDKTGVFDGYIKLTVT 420 Query: 417 GDRSTFTVTATYIPHFGERIVEINGFNIDFYPTGHLVYIQHQDTTGVIGRVGRILGDNDI 476 + T +V T R ++I G N+D H++YI + D G+IG +G LG + Sbjct: 421 TESMTRSVAGTVFSDGKPRFIQIKGINLDADVGSHMIYITNTDVPGMIGFIGTTLGAAGV 480 Query: 477 NIATMQVGRKEKGGEAIMMLSFDRHLEDKIVKELT 511 NIA Q+GR ++GG+AI +L D ++D ++ ELT Sbjct: 481 NIANFQLGRDKQGGDAIALLYVDGKVDDAVLAELT 515 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: 675 Number of extensions: 26 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: 531 Length adjustment: 35 Effective length of query: 490 Effective length of database: 496 Effective search space: 243040 Effective search space used: 243040 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_012758842.1 RLEG_RS17215 (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.20299.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.4e-207 674.0 7.1 9.5e-207 673.8 7.1 1.0 1 lcl|NCBI__GCF_000023185.1:WP_012758842.1 RLEG_RS17215 phosphoglycerate de Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023185.1:WP_012758842.1 RLEG_RS17215 phosphoglycerate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 673.8 7.1 9.5e-207 9.5e-207 1 521 [. 4 524 .. 4 528 .. 0.98 Alignments for each domain: == domain 1 score: 673.8 bits; conditional E-value: 9.5e-207 TIGR01327 1 kvlvadklseegiellkekelevdvktgl..skeellekikdydalivRSatkvteelleaaekLkvig 67 +vlv+d+lse+++++++++++evd + +l +k+ lle+i +yd+l +RSatkvte+++e a++Lkv+g lcl|NCBI__GCF_000023185.1:WP_012758842.1 4 RVLVSDELSETAVQIFRDRGVEVDFEPQLgkDKDRLLEVIGKYDGLAIRSATKVTEKIIEGATNLKVVG 72 79*********************9988772266789********************************* PP TIGR01327 68 RaGvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtEl 136 RaG+GvDN+di+aa+++Gi+v+N+P gn+i++aE+a+al++a+aR++p+ad+s++++kWe++kf+G+E+ lcl|NCBI__GCF_000023185.1:WP_012758842.1 73 RAGIGVDNVDIPAASRRGIIVMNTPFGNSITTAEHAIALMFAVARQLPAADTSTQAGKWEKSKFMGVEI 141 ********************************************************************* PP TIGR01327 137 ygktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltk 205 +gktlGviG+G+iGs+v ra +l+m+v+ayDP++s+e+ae++gv++++ l+el+a+aD+it+HvP t+ lcl|NCBI__GCF_000023185.1:WP_012758842.1 142 TGKTLGVIGAGNIGSIVCARAIGLKMHVVAYDPFLSKERAEEMGVTKVE-LEELFARADFITLHVPMTD 209 **********************************************666.******************* PP TIGR01327 206 etkgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvv 274 +t+g+++ke+lak+K+gv+i+NcaRGG++dE+AL+ea+++g+v++aa+Dvfe EP+++++l+ l+nvv lcl|NCBI__GCF_000023185.1:WP_012758842.1 210 KTRGILNKEALAKTKPGVRIINCARGGLVDEAALAEAIKSGHVAGAAFDVFEVEPAKESPLFGLPNVVC 278 ********************************************************************* PP TIGR01327 275 tpHlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllke 343 tpHlgAst+Eaqenva++vae++ ++l + +v++a+N+p+++aee+ lkp+++la+ lG++++q+++e lcl|NCBI__GCF_000023185.1:WP_012758842.1 279 TPHLGASTTEAQENVALQVAEQMADYLVNGAVSNAINMPSITAEEAPILKPFIRLADVLGAFVGQVTEE 347 ********************************************************************* PP TIGR01327 344 avkkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknll 412 +k++e+ + G a++++ +ltsa+l+gl++++++ +vn+v+A+++ ke+gi ++e k++++ ++ ++ lcl|NCBI__GCF_000023185.1:WP_012758842.1 348 PIKEIEILYDGITANMNTRALTSAALAGLIRPQVA-DVNMVSAPIMIKEKGIVLSEVKRDKTGVFDGYI 415 **********************************9.8******************************** PP TIGR01327 413 evkveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNias 481 +++v++++ ++svagtv+++ +pr ++i+g+++d ++++i+n+D+pG+ig +g++lg ag+Nia+ lcl|NCBI__GCF_000023185.1:WP_012758842.1 416 KLTVTTESMTRSVAGTVFSDGKPRFIQIKGINLDADVGSHMIYITNTDVPGMIGFIGTTLGAAGVNIAN 484 ********************************************************************* PP TIGR01327 482 mqlgrkekggealmllslDeevseevleeikevpeiksvk 521 +qlgr+++gg+a++ll +D +v++ vl+e+++ ++++++k lcl|NCBI__GCF_000023185.1:WP_012758842.1 485 FQLGRDKQGGDAIALLYVDGKVDDAVLAELTAHQAVRQAK 524 ********************************99999887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (525 nodes) Target sequences: 1 (531 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: 9.83 // [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