Align phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized)
to candidate WP_036262805.1 DL86_RS14275 phosphoglycerate dehydrogenase
Query= CharProtDB::CH_004924 (525 letters) >NCBI__GCF_000746085.1:WP_036262805.1 Length = 528 Score = 418 bits (1074), Expect = e-121 Identities = 217/524 (41%), Positives = 327/524 (62%), Gaps = 5/524 (0%) Query: 3 RVLVSDKMSNDGLQPL----IESDFIEIVQKNVADAEDELHTFDALLVRSATKVTEDLFN 58 RVL+SD +S + ++ DF + K+ + FD L +RSATKVT + + Sbjct: 4 RVLISDALSLAAVAIFKERGVDVDFQPQLGKDKEKLAAVIGAFDGLAIRSATKVTAKILD 63 Query: 59 KMTSLKIVGRAGVGVDNIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQAN 118 + T LK++GRAG+GVDN+DI AT GVIV+N P GN+I+TAEH A++ +L R IPQA+ Sbjct: 64 QATRLKVIGRAGIGVDNVDIPAATAKGVIVMNTPFGNSITTAEHAIALMFALARQIPQAD 123 Query: 119 ISVKSREWNRTAYVGSELYGKTLGIVGLGRIGSEIAQRRGAFGMTVHVFDPFLTEERAKK 178 S ++ +W + ++G E+ GKTLG++G G IGS +A+R M V +DPFLT ERA Sbjct: 124 ASTQAGKWEKNRFMGVEITGKTLGVIGCGNIGSIVAERAIGLHMHVLAYDPFLTPERALA 183 Query: 179 IGVNSRTFEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEAAL 238 +GV E +L ADIIT+H P+T +TK +L+ E + KTKKGVR+INCARGG+ DE AL Sbjct: 184 LGVEKVELEPLLARADIITLHAPMTPQTKNILSAENLVKTKKGVRIINCARGGLADEKAL 243 Query: 239 LEALENGHVAGAALDVFEVEPPVDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSEEVLQ 298 L++GHVAGAA DVF EP +N L HP V+ TPHLGAST EAQ NVA QV+E++ Sbjct: 244 RALLDSGHVAGAAFDVFVSEPATENPLFGHPNVVCTPHLGASTNEAQENVALQVAEQMSD 303 Query: 299 FAKGLPVMSAINLPAMTKDEFAKIKPYHQIAGKIGSLVSQCMKEPVQDVAIQYEGTIAKL 358 + + +A+N P++T +E K+KP+ +A ++GS Q + + V I YEG++A+L Sbjct: 304 YLIRGAISNAVNFPSITAEEAPKLKPFIALAERLGSFAGQLVDSAIMKVTITYEGSVAEL 363 Query: 359 ETSFITKALLSGFLKPRVDSTVNEVNAGGVAKERGISFSEKISSSESGYDNCISVKVTGD 418 +T +T A ++G L+P + + VN V+A VAKERG++ E ++++ Y++ I++ V + Sbjct: 364 KTKALTAAAIAGLLRPLL-ADVNVVSAPLVAKERGVAIDEVTRAADADYESLITLSVETE 422 Query: 419 RSTFTVTATYIPHFGERIVEINGFNIDFYPTGHLVYIQHQDTTGVIGRVGRILGDNDINI 478 +V+ T RI+ ING +D ++Y+ ++D G IGR +LG+ +NI Sbjct: 423 AHKRSVSGTVFHDGRPRIISINGIQVDALVAPAMIYVSNEDRPGFIGRFASVLGNAGVNI 482 Query: 479 ATMQVGRKEKGGEAIMMLSFDRHLEDKIVKELTNVPDIVSVKLI 522 AT +GR GG A+ ++ D ++ E+ +P + K + Sbjct: 483 ATFALGRDRAGGSAVALVEVDGVAPGDVLVEVEKLPGVKEAKAL 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: 611 Number of extensions: 25 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_036262805.1 DL86_RS14275 (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.22165.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-205 668.2 4.4 5.2e-205 668.1 4.4 1.0 1 lcl|NCBI__GCF_000746085.1:WP_036262805.1 DL86_RS14275 phosphoglycerate de Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000746085.1:WP_036262805.1 DL86_RS14275 phosphoglycerate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 668.1 4.4 5.2e-205 5.2e-205 1 523 [. 4 526 .. 4 528 .] 0.98 Alignments for each domain: == domain 1 score: 668.1 bits; conditional E-value: 5.2e-205 TIGR01327 1 kvlvadklseegiellkekelevdvktgl..skeellekikdydalivRSatkvteelleaaekLkvig 67 +vl++d ls ++++++ke++++vd + +l +ke+l ++i +d+l +RSatkvt+++l++a++Lkvig lcl|NCBI__GCF_000746085.1:WP_036262805.1 4 RVLISDALSLAAVAIFKERGVDVDFQPQLgkDKEKLAAVIGAFDGLAIRSATKVTAKILDQATRLKVIG 72 79**********************998773367789999****************************** PP TIGR01327 68 RaGvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtEl 136 RaG+GvDN+di+aat+kG++v+N+P gn+i++aE+a+al++alaR+ipqad+s++++kWe+++f+G+E+ lcl|NCBI__GCF_000746085.1:WP_036262805.1 73 RAGIGVDNVDIPAATAKGVIVMNTPFGNSITTAEHAIALMFALARQIPQADASTQAGKWEKNRFMGVEI 141 ********************************************************************* PP TIGR01327 137 ygktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltk 205 +gktlGviG G+iGs+va+ra +l+m+vlayDP++++e+a lgve+++ l+ lla+aD+it+H+P t+ lcl|NCBI__GCF_000746085.1:WP_036262805.1 142 TGKTLGVIGCGNIGSIVAERAIGLHMHVLAYDPFLTPERALALGVEKVE-LEPLLARADIITLHAPMTP 209 **********************************************666.******************* PP TIGR01327 206 etkgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvv 274 +tk+++++e+l k+Kkgv+i+NcaRGG+ dEkAL +l++g+v++aa+Dvf +EP+t+n+l+ ++nvv lcl|NCBI__GCF_000746085.1:WP_036262805.1 210 QTKNILSAENLVKTKKGVRIINCARGGLADEKALRALLDSGHVAGAAFDVFVSEPATENPLFGHPNVVC 278 ********************************************************************* PP TIGR01327 275 tpHlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllke 343 tpHlgAst+Eaqenva++vae+++++l + ++avN p+++aee+ klkp+++lae+lG++a+ql+++ lcl|NCBI__GCF_000746085.1:WP_036262805.1 279 TPHLGASTNEAQENVALQVAEQMSDYLIRGAISNAVNFPSITAEEAPKLKPFIALAERLGSFAGQLVDS 347 ********************************************************************* PP TIGR01327 344 avkkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknll 412 a+ kv++t+eG +ae ++++lt+a+++gll++ l+ +vn+v+A+ vakerg+ + e ++++ dy++l+ lcl|NCBI__GCF_000746085.1:WP_036262805.1 348 AIMKVTITYEGSVAELKTKALTAAAIAGLLRPLLA-DVNVVSAPLVAKERGVAIDEVTRAADADYESLI 415 ********************************998.8******************************** PP TIGR01327 413 evkveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNias 481 ++ ve++ +++sv+gtv+++ pri+ i+g++vd ++++++n+D+pG+ig+ +s+lg+ag+Nia+ lcl|NCBI__GCF_000746085.1:WP_036262805.1 416 TLSVETEAHKRSVSGTVFHDGRPRIISINGIQVDALVAPAMIYVSNEDRPGFIGRFASVLGNAGVNIAT 484 ********************************************************************* PP TIGR01327 482 mqlgrkekggealmllslDeevseevleeikevpeiksvklv 523 ++lgr+++gg+a++l+++D ++ +vl e++++p +k++k++ lcl|NCBI__GCF_000746085.1:WP_036262805.1 485 FALGRDRAGGSAVALVEVDGVAPGDVLVEVEKLPGVKEAKAL 526 *************************************99876 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 7.17 // [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