Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate WP_015412066.1 MM_RS09090 phosphoglycerate dehydrogenase
Query= uniprot:Q6LWW6 (523 letters) >NCBI__GCF_000007065.1:WP_015412066.1 Length = 523 Score = 483 bits (1242), Expect = e-141 Identities = 246/522 (47%), Positives = 359/522 (68%), Gaps = 1/522 (0%) Query: 3 KILITDPLHESAVEILKQAGEVEVATGLTVEELKLKIKDVDALVIRSGTTATREIIEASE 62 K+L++D L +EILK+ +++V TGL +EL KIK DALVIRSGT T+ IIEA++ Sbjct: 2 KVLVSDSLSNEGLEILKEHFDIDVCTGLCEDELVEKIKGYDALVIRSGTQVTQRIIEAAD 61 Query: 63 NLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAAARNIPQATASI 122 NLK+I RAGVGVDNVD+DAAT+KGI+V NAP+ + IS AE MM++ +RNIPQA AS+ Sbjct: 62 NLKIIGRAGVGVDNVDVDAATKKGIIVANAPEGNMISAAEHTIAMMMSMSRNIPQANASL 121 Query: 123 KSGKWDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVASELGI 182 K+ +W R F G+E+ GKTLG++GLGRIG +VAKRA M ++ YDP+I E A ELG+ Sbjct: 122 KAREWKRNKFMGVEVKGKTLGVIGLGRIGSEVAKRAAGLEMNLMGYDPFISEKRAMELGV 181 Query: 183 KLLTVDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNCARGGLIDEAALYDA 242 KL TV+E+ +D+IT+H PL +T++++ EQ ALMK + ++NCARGG+I+E AL A Sbjct: 182 KLATVNEIAKEADYITVHTPLIKETRNILDDEQFALMKKGVRVLNCARGGIINEEALARA 241 Query: 243 LNSGKIKAAALDVFEQEPPKESPLLTLNNLIGTPHQGASTEEAQLSAGTIVAEQTVKILK 302 L SGK+ AA+DVF +EPP SPLL +N+I TPH GAST+EAQ++ +A++ V +L Sbjct: 242 LESGKVGGAAIDVFVEEPPFSSPLLNFDNVIVTPHLGASTQEAQVNVAIDIAKEVVSVLT 301 Query: 303 GESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMGGLAKEKTE 362 G SA+N +N+P V E M L PY+ L+E MG +A Q +D++ E +EI Y G ++ + T Sbjct: 302 GGSAKNAINIPSVKPEAMAVLAPYIRLSELMGKIAGQLVDSNYEKVEIAYNGEISGKDTR 361 Query: 363 ILKRSFLKGILAPILLAGVNLVNAPVIAKSRNIKIAEG-TMSESDYGNSIKISAKGENDE 421 L S LKG+L + +GVN VNAP++AKSR I + E + S +Y +++ I Sbjct: 362 PLTVSALKGLLEMAVGSGVNYVNAPILAKSRKIAVVESKSESAEEYSSTVSIRLSSGEST 421 Query: 422 ISIIGSIEHNEVVFREINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEHGINIAGMQ 481 + G++ +E I+ ++DI P G + KHI++P ++G ++LG++ INI+GMQ Sbjct: 422 KMVAGTVVGDEPKIVSIDDDKVDIFPAGRMIFAKHINKPNVIGPCCMVLGKNNINISGMQ 481 Query: 482 VGRREPGGHSIMFLDIDHMISDEVLDEIRKMENVRAAKSINI 523 VGR E GG ++M L++D +SD +LDE+R++ + AK + + Sbjct: 482 VGRSEVGGVTMMVLNVDTDVSDAILDEVRQVPGILNAKLVTL 523 Lambda K H 0.316 0.134 0.364 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: 740 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: 523 Length of database: 523 Length adjustment: 35 Effective length of query: 488 Effective length of database: 488 Effective search space: 238144 Effective search space used: 238144 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_015412066.1 MM_RS09090 (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.1102567.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.9e-212 690.5 14.0 8.9e-212 690.4 14.0 1.0 1 NCBI__GCF_000007065.1:WP_015412066.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000007065.1:WP_015412066.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 690.4 14.0 8.9e-212 8.9e-212 1 525 [] 2 523 .] 2 523 .] 0.99 Alignments for each domain: == domain 1 score: 690.4 bits; conditional E-value: 8.9e-212 TIGR01327 1 kvlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaGvGv 73 kvlv+d+ls+eg+e+lke+ +++dv tgl ++el+ekik ydal++RS t+vt+ ++eaa++Lk+igRaGvGv NCBI__GCF_000007065.1:WP_015412066.1 2 KVLVSDSLSNEGLEILKEH-FDIDVCTGLCEDELVEKIKGYDALVIRSGTQVTQRIIEAADNLKIIGRAGVGV 73 7***************966.8**************************************************** PP TIGR01327 74 DNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygktlGviGl 146 DN+d++aatkkGi+v NaPegn isaaE+++a++++++R+ipqa++s+k+++W+r+kf+G+E++gktlGviGl NCBI__GCF_000007065.1:WP_015412066.1 74 DNVDVDAATKKGIIVANAPEGNMISAAEHTIAMMMSMSRNIPQANASLKAREWKRNKFMGVEVKGKTLGVIGL 146 ************************************************************************* PP TIGR01327 147 GriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelakm 219 GriGsevakra++l+m++++yDP+ise++a +lgv+ l++++e+++eaD itvH+Pl ket+++++ e++a m NCBI__GCF_000007065.1:WP_015412066.1 147 GRIGSEVAKRAAGLEMNLMGYDPFISEKRAMELGVK-LATVNEIAKEADYITVHTPLIKETRNILDDEQFALM 218 ************************************.888********************************* PP TIGR01327 220 KkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpHlgAsteEaqenvave 292 Kkgv+++NcaRGGii+E+AL+ ale+gkv +aa+Dvf +EPp +++ll++dnv+vtpHlgAst+Eaq nva++ NCBI__GCF_000007065.1:WP_015412066.1 219 KKGVRVLNCARGGIINEEALARALESGKVGGAAIDVFVEEPPFSSPLLNFDNVIVTPHLGASTQEAQVNVAID 291 ************************************************************************* PP TIGR01327 293 vaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeesellt 365 +a+ev+++l+g ++++a+N+p+++ e+++ l+py++l+e +Gk+a+ql++++ +kve++++Ge++ +++ +lt NCBI__GCF_000007065.1:WP_015412066.1 292 IAKEVVSVLTGGSAKNAINIPSVKPEAMAVLAPYIRLSELMGKIAGQLVDSNYEKVEIAYNGEISGKDTRPLT 364 ************************************************************************* PP TIGR01327 366 sallkgllkevleeevnlvnAkavakergitveeskeeesedyknllevkveadkgevsvagtvleekepriv 438 ++lkgll+ ++ + vn+vnA+++ak r+i v esk+e++e+y++++++++++ ++++ vagtv++ +ep+iv NCBI__GCF_000007065.1:WP_015412066.1 365 VSALKGLLEMAVGSGVNYVNAPILAKSRKIAVVESKSESAEEYSSTVSIRLSSGESTKMVAGTVVG-DEPKIV 436 ******************************************************************.5***** PP TIGR01327 439 eidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseevleei 511 id+ +vd+ p g ++++k+ +kp vig +++lg+++iNi +mq+gr+e gg ++m+l++D +vs+ +l+e+ NCBI__GCF_000007065.1:WP_015412066.1 437 SIDDDKVDIFPAGRMIFAKHINKPNVIGPCCMVLGKNNINISGMQVGRSEVGGVTMMVLNVDTDVSDAILDEV 509 ************************************************************************* PP TIGR01327 512 kevpeiksvklvel 525 ++vp i ++klv+l NCBI__GCF_000007065.1:WP_015412066.1 510 RQVPGILNAKLVTL 523 **********9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (525 nodes) Target sequences: 1 (523 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 27.25 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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