Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate WP_011869563.1 MMARC5_RS09360 phosphoglycerate dehydrogenase
Query= uniprot:Q6LWW6 (523 letters) >NCBI__GCF_000016125.1:WP_011869563.1 Length = 523 Score = 966 bits (2497), Expect = 0.0 Identities = 497/523 (95%), Positives = 510/523 (97%) Query: 1 MSKILITDPLHESAVEILKQAGEVEVATGLTVEELKLKIKDVDALVIRSGTTATREIIEA 60 MSK+LITDPLHESAVEILKQAGEVEVATGL VEE+KLKIKD DALV+RSGTT TREIIEA Sbjct: 1 MSKVLITDPLHESAVEILKQAGEVEVATGLNVEEIKLKIKDADALVVRSGTTVTREIIEA 60 Query: 61 SENLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAAARNIPQATA 120 SENLKVIARAGVG+DNVDLDAATEKGIVVVNAPDASSISVAELLFGMML+AARNIPQATA Sbjct: 61 SENLKVIARAGVGIDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLSAARNIPQATA 120 Query: 121 SIKSGKWDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVASEL 180 SIK G+WDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVASEL Sbjct: 121 SIKKGEWDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVASEL 180 Query: 181 GIKLLTVDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNCARGGLIDEAALY 240 GIKLLTVDELC SDFITLHVPLTPKTKHMIGK+QIALMKSNMVIMNCARGGLIDE ALY Sbjct: 181 GIKLLTVDELCAASDFITLHVPLTPKTKHMIGKDQIALMKSNMVIMNCARGGLIDEDALY 240 Query: 241 DALNSGKIKAAALDVFEQEPPKESPLLTLNNLIGTPHQGASTEEAQLSAGTIVAEQTVKI 300 +ALNSGKIKAA LDVFEQEPPKESPLLTLNNLIGTPHQGASTEEAQLSAGTIVAEQTVKI Sbjct: 241 EALNSGKIKAAGLDVFEQEPPKESPLLTLNNLIGTPHQGASTEEAQLSAGTIVAEQTVKI 300 Query: 301 LKGESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMGGLAKEK 360 LKGESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMGGLA EK Sbjct: 301 LKGESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMGGLANEK 360 Query: 361 TEILKRSFLKGILAPILLAGVNLVNAPVIAKSRNIKIAEGTMSESDYGNSIKISAKGEND 420 TEI+KRSFLKGILAPILLAGVNLVNAPVIAKSRNIK+AEGTMSESDYGN IKI AKGEND Sbjct: 361 TEIIKRSFLKGILAPILLAGVNLVNAPVIAKSRNIKLAEGTMSESDYGNLIKIVAKGEND 420 Query: 421 EISIIGSIEHNEVVFREINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEHGINIAGM 480 EISIIGSIEHNE+VFREINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEHGINIAGM Sbjct: 421 EISIIGSIEHNEIVFREINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEHGINIAGM 480 Query: 481 QVGRREPGGHSIMFLDIDHMISDEVLDEIRKMENVRAAKSINI 523 QVGRREPGGHSIMFLD+DHMISDEV+ EI KMENVRAAKSINI Sbjct: 481 QVGRREPGGHSIMFLDVDHMISDEVMAEITKMENVRAAKSINI 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: 1058 Number of extensions: 30 Number of successful extensions: 1 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_011869563.1 MMARC5_RS09360 (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.849540.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-211 689.6 14.4 1.7e-211 689.5 14.4 1.0 1 NCBI__GCF_000016125.1:WP_011869563.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000016125.1:WP_011869563.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 689.5 14.4 1.7e-211 1.7e-211 1 524 [. 3 522 .. 3 523 .] 0.99 Alignments for each domain: == domain 1 score: 689.5 bits; conditional E-value: 1.7e-211 TIGR01327 1 kvlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaGvGv 73 kvl++d+l+e+++e+lk+ + ev+v+tgl+ ee+ kikd+dal+vRS t+vt+e++ea e+Lkvi+RaGvG+ NCBI__GCF_000016125.1:WP_011869563.1 3 KVLITDPLHESAVEILKQAG-EVEVATGLNVEEIKLKIKDADALVVRSGTTVTREIIEASENLKVIARAGVGI 74 7****************998.**************************************************** PP TIGR01327 74 DNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygktlGviGl 146 DN+d++aat+kGi+vvNaP++++is+aEl + ++l++aR+ipqa++s+k+++W+rk+f+G+E+ygktlG++Gl NCBI__GCF_000016125.1:WP_011869563.1 75 DNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLSAARNIPQATASIKKGEWDRKSFKGMEIYGKTLGIVGL 147 ************************************************************************* PP TIGR01327 147 GriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelakm 219 GriG++vakra+a+gm+++ayDPyi+e+ a++lg++l ++del+a +D+it+HvPlt++tk++igk+++a m NCBI__GCF_000016125.1:WP_011869563.1 148 GRIGQQVAKRAQAFGMTIVAYDPYIPEDVASELGIKL-LTVDELCAASDFITLHVPLTPKTKHMIGKDQIALM 219 ************************************5.55********************************* PP TIGR01327 220 KkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpHlgAsteEaqenvave 292 K++++i+NcaRGG+idE+AL+eal++gk++aa+lDvfe+EPp++++ll+l+n++ tpH+gAsteEaq ++++ NCBI__GCF_000016125.1:WP_011869563.1 220 KSNMVIMNCARGGLIDEDALYEALNSGKIKAAGLDVFEQEPPKESPLLTLNNLIGTPHQGASTEEAQLSAGTI 292 ************************************************************************* PP TIGR01327 293 vaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeesellt 365 vae+ +++lkge++e++vNlp++ +e+++klkpy+ laek+G++a+q+l+++++ +e+t+ G la+e++e+++ NCBI__GCF_000016125.1:WP_011869563.1 293 VAEQTVKILKGESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMGGLANEKTEIIK 365 ************************************************************************* PP TIGR01327 366 sallkgllkevleeevnlvnAkavakergitveeskeeesedyknllevkveadkgevsvagtvleekepriv 438 +++lkg+l ++l + vnlvnA+++ak r+i++ e + +e +dy nl+++ ++++++e+s+ g++ + +e NCBI__GCF_000016125.1:WP_011869563.1 366 RSFLKGILAPILLAGVNLVNAPVIAKSRNIKLAEGTMSE-SDYGNLIKIVAKGENDEISIIGSIEH-NEIVFR 436 *********************************988776.9*********************9877.5999** PP TIGR01327 439 eidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseevleei 511 ei+g+++d++peg++ iik+ D+pG++gkvg llge+giNia+mq+gr+e gg+++m l +D+ +s+ev++ei NCBI__GCF_000016125.1:WP_011869563.1 437 EINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEHGINIAGMQVGRREPGGHSIMFLDVDHMISDEVMAEI 509 ************************************************************************* PP TIGR01327 512 kevpeiksvklve 524 +++++++ +k ++ NCBI__GCF_000016125.1:WP_011869563.1 510 TKMENVRAAKSIN 522 *******999987 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 15.88 // [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