Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate WP_013818165.1 METME_RS07460 phosphoglycerate dehydrogenase
Query= uniprot:Q6LWW6 (523 letters) >NCBI__GCF_000214665.1:WP_013818165.1 Length = 527 Score = 403 bits (1035), Expect = e-116 Identities = 213/527 (40%), Positives = 332/527 (62%), Gaps = 8/527 (1%) Query: 1 MSKILITDPLHESAVEIL-KQAG-EVEVATGLTVEELKLKIKDVDALVIRSGTTATREII 58 M KILI+D L + + L +QAG ++ + TGL+ EL I + DAL+IRS T T ++ Sbjct: 1 MKKILISDKLADDGINFLNEQAGIQIHIQTGLSEAELCEIIPEYDALLIRSDTQVTANVL 60 Query: 59 EASENLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAAARNIPQA 118 +A++ LKV+ RAG+GVDNVDL A E+GI+V+N PDA++ + AEL M + +RN+P A Sbjct: 61 KAAKKLKVVGRAGIGVDNVDLAVAMEQGIIVMNTPDANATTTAELAIAHMFSLSRNLPIA 120 Query: 119 TASIKSGKWDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVAS 178 S++ GKW+R G EI KTL I+G G IG+ VA+R GM ++AYDP++ ++ Sbjct: 121 NQSVRDGKWERSKLVGAEISHKTLAILGFGTIGRIVAQRGNGLGMRVIAYDPFVAPEIFE 180 Query: 179 ELGIKLLTVDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNCARGGLIDEAA 238 + G +++ +D L +D++TLH PL KT+++IG+EQ A+MK ++NCARGGL+DEAA Sbjct: 181 KCGAEMVDLDTLVKHADYLTLHCPLLEKTRNVIGREQFAMMKKTARLINCARGGLVDEAA 240 Query: 239 LYDALNSGKIKAAALDVFEQEPPKESPLLTLNNLIGTPHQGASTEEAQLSAGTIVAEQTV 298 LYDAL G+I AALDV+EQEPP++SPLL+L+N++ TPH GAST+EAQ++ +A Q V Sbjct: 241 LYDALKEGRIAGAALDVYEQEPPRDSPLLSLDNVVFTPHLGASTKEAQVAVSVEIARQVV 300 Query: 299 KILKGESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMGGLAK 358 K L+ A N +NLP + E++K+ +P+M LA +G + + +D I+ LE+ G A Sbjct: 301 KYLQTGEAINALNLPRLSAEELKQAQPFMNLAHILGKVLLGLIDQPIQKLEVAVFGKAAL 360 Query: 359 EKTEILKRSFLKGILAPILLAGVNLVNAPVIAKSRNIKIAEGTMSESD-YGNSIKISAKG 417 K + + G+LA VN VN IAK + I + E E++ Y + IKI+ Sbjct: 361 GKIRPISAEAMVGLLAGQFDTPVNRVNVENIAKRQGIALVESQTEEAEGYQSLIKITGHC 420 Query: 418 ENDEISIIGSI---EHNEVVFREINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEHG 474 + +S+ G++ H +V IN + +++ PEG + + +H D+PG++ + +LG Sbjct: 421 VDKSVSLAGTLLGDHHPRLV--SINHFEIEVVPEGALVVTRHDDKPGVIAAISSILGVSN 478 Query: 475 INIAGMQVGRREPGGHSIMFLDIDHMISDEVLDEIRKMENVRAAKSI 521 INI MQV + S+M + + +S++VL + + V++A+ I Sbjct: 479 INITRMQVSVADENQLSMMVISVSDPLSEQVLKAVCDVPAVQSARQI 525 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: 649 Number of extensions: 25 Number of successful extensions: 4 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: 527 Length adjustment: 35 Effective length of query: 488 Effective length of database: 492 Effective search space: 240096 Effective search space used: 240096 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_013818165.1 METME_RS07460 (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.29004.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-187 610.1 8.4 2.1e-187 610.0 8.4 1.0 1 lcl|NCBI__GCF_000214665.1:WP_013818165.1 METME_RS07460 phosphoglycerate d Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000214665.1:WP_013818165.1 METME_RS07460 phosphoglycerate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 610.0 8.4 2.1e-187 2.1e-187 1 525 [] 3 527 .] 3 527 .] 0.99 Alignments for each domain: == domain 1 score: 610.0 bits; conditional E-value: 2.1e-187 TIGR01327 1 kvlvadklseegie.llkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigR 68 k+l++dkl+++gi+ l ++ +++++++tgls++el e+i++ydal++RS t+vt+++l+aa+kLkv+gR lcl|NCBI__GCF_000214665.1:WP_013818165.1 3 KILISDKLADDGINfLNEQAGIQIHIQTGLSEAELCEIIPEYDALLIRSDTQVTANVLKAAKKLKVVGR 71 79************8889999************************************************ PP TIGR01327 69 aGvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtEly 137 aG+GvDN+d+ a ++Gi+v+N+P++n ++aEla+a++++l+R++p a++sv+++kWer+k +G E+ lcl|NCBI__GCF_000214665.1:WP_013818165.1 72 AGIGVDNVDLAVAMEQGIIVMNTPDANATTTAELAIAHMFSLSRNLPIANQSVRDGKWERSKLVGAEIS 140 ********************************************************************* PP TIGR01327 138 gktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltke 206 +ktl ++G+G iG +va+r ++lgm+v+ayDP++++e +ek g e + dld+l+++aD +t+H Pl ++ lcl|NCBI__GCF_000214665.1:WP_013818165.1 141 HKTLAILGFGTIGRIVAQRGNGLGMRVIAYDPFVAPEIFEKCGAE-MVDLDTLVKHADYLTLHCPLLEK 208 *********************************************.677******************** PP TIGR01327 207 tkgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvt 275 t+++ig+e++a mKk+++++NcaRGG++dE+AL++al+eg++++aalDv+e+EPp d++ll+ldnvv t lcl|NCBI__GCF_000214665.1:WP_013818165.1 209 TRNVIGREQFAMMKKTARLINCARGGLVDEAALYDALKEGRIAGAALDVYEQEPPRDSPLLSLDNVVFT 277 ********************************************************************* PP TIGR01327 276 pHlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkea 344 pHlgAst+Eaq +v+ve+a +v+++l++ + +a+Nlp l+aeel++ +p+++la+ lGk+ l ++ lcl|NCBI__GCF_000214665.1:WP_013818165.1 278 PHLGASTKEAQVAVSVEIARQVVKYLQTGEAINALNLPRLSAEELKQAQPFMNLAHILGKVLLGLIDQP 346 ********************************************************************* PP TIGR01327 345 vkkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknlle 413 ++k+ev++ G+ a + ++++ ++ gll + ++ vn vn + +ak +gi + es++ee+e y++l++ lcl|NCBI__GCF_000214665.1:WP_013818165.1 347 IQKLEVAVFGKAALGKIRPISAEAMVGLLAGQFDTPVNRVNVENIAKRQGIALVESQTEEAEGYQSLIK 415 ********************************************************************* PP TIGR01327 414 vkveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasm 482 ++ + +++vs+agt+l++++pr+v i++fe+++ peg+l+++++ DkpGvi+ ++s+lg +iNi m lcl|NCBI__GCF_000214665.1:WP_013818165.1 416 ITGHCVDKSVSLAGTLLGDHHPRLVSINHFEIEVVPEGALVVTRHDDKPGVIAAISSILGVSNINITRM 484 ********************************************************************* PP TIGR01327 483 qlgrkekggealmllslDeevseevleeikevpeiksvklvel 525 q++ +++ ++m++s+ +++se+vl+++ +vp+++s++ + l lcl|NCBI__GCF_000214665.1:WP_013818165.1 485 QVSVADENQLSMMVISVSDPLSEQVLKAVCDVPAVQSARQIVL 527 *************************************999875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (525 nodes) Target sequences: 1 (527 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: 11.12 // [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