Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate WP_012818167.1 ADEG_RS00050 phosphoglycerate dehydrogenase
Query= uniprot:Q6LWW6 (523 letters) >NCBI__GCF_000024605.1:WP_012818167.1 Length = 527 Score = 475 bits (1222), Expect = e-138 Identities = 244/525 (46%), Positives = 346/525 (65%), Gaps = 4/525 (0%) Query: 1 MSKILITDPLHESAVEILKQAGEVEV--ATGLTVEELKLKIKDVDALVIRSGTTATREII 58 M ++L+TD + ++ L +A +VEV L EELK I + DAL++RS T T ++ Sbjct: 1 MYRVLVTDGVSPEGLKALTEAPDVEVDFRPTLNEEELKEIIGEYDALIVRSATKVTAAVL 60 Query: 59 EASENLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAAARNIPQA 118 E + LK+I RAGVGVDN+D+ AAT KGI+V NAP ++++ AE G+ML+ ARNIP+A Sbjct: 61 EKARRLKIIGRAGVGVDNIDVKAATAKGIIVANAPGGNTVAAAEHTIGLMLSLARNIPEA 120 Query: 119 TASIKSGKWDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVAS 178 A KSG WDRKSF G+E+ GK LGI+GLGRIG +VAKRAQA M I+AYDPYIPE+ A Sbjct: 121 CARTKSGVWDRKSFMGVELRGKVLGIIGLGRIGSEVAKRAQAMEMKIIAYDPYIPEERAR 180 Query: 179 ELGIKLLTVDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNCARGGLIDEAA 238 +L +KL+ +D L +DFIT+H+PL+ +T H+I +E MK + ++NCARGG++DE A Sbjct: 181 DLRVKLVPLDTLLQEADFITIHIPLSKETYHLIDREAFVKMKPGVRLINCARGGIVDEEA 240 Query: 239 LYDALNSGKIKAAALDVFEQEPPKESPLLTLNNLIGTPHQGASTEEAQLSAGTIVAEQTV 298 LY+AL GK+ AALDVFE+EP PL +L N++ TPH GAST EAQL+ ++A++ + Sbjct: 241 LYEALKEGKVAGAALDVFEKEPVTSHPLFSLPNVVVTPHLGASTVEAQLAVAEVIAQEVL 300 Query: 299 KILKGESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMGGLAK 358 L+G + VNLP + E + + P++ LAEK+G A Q + I +E+ Y G +A+ Sbjct: 301 TALRGGFVRHAVNLPYLRPEVLPVVGPFLPLAEKLGLFAAQLVSGRINQVEVNYSGEIAR 360 Query: 359 EKTEILKRSFLKGILAPILLAGVNLVNAPVIAKSRNIKIAEGTMS-ESDYGNSIKISAKG 417 T +L + LKG+L+ L +N VNAP +AK R IK+ E E +Y N I + + Sbjct: 361 YDTSLLNTAVLKGVLSVALQDTINYVNAPEVAKQRGIKVKETKQEREEEYVNLISVKVEA 420 Query: 418 ENDEISIIGS-IEHNEVVFREINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEHGIN 476 E ++ G+ + E EI+GYR+D PEG + I H+DRP ++G++G L+G H IN Sbjct: 421 PEGEHTVAGTLVRGKEPRVVEIDGYRVDAVPEGYVLFIPHLDRPRIIGRIGTLIGAHDIN 480 Query: 477 IAGMQVGRREPGGHSIMFLDIDHMISDEVLDEIRKMENVRAAKSI 521 IA MQVGR+E GG +IM L +D + +E L EI K+ENV K + Sbjct: 481 IAAMQVGRKEIGGKAIMLLSVDSPVPEETLREIAKVENVLDVKML 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: 718 Number of extensions: 32 Number of successful extensions: 3 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_012818167.1 ADEG_RS00050 (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.30953.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.7e-221 720.1 3.4 9.7e-221 720.0 3.4 1.0 1 lcl|NCBI__GCF_000024605.1:WP_012818167.1 ADEG_RS00050 phosphoglycerate de Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000024605.1:WP_012818167.1 ADEG_RS00050 phosphoglycerate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 720.0 3.4 9.7e-221 9.7e-221 1 523 [. 3 525 .. 3 527 .] 0.99 Alignments for each domain: == domain 1 score: 720.0 bits; conditional E-value: 9.7e-221 TIGR01327 1 kvlvadklseegie.llkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigR 68 +vlv+d +s+eg++ l++ ++evd + l++eel e+i +ydalivRSatkvt+ +le+a++Lk+igR lcl|NCBI__GCF_000024605.1:WP_012818167.1 3 RVLVTDGVSPEGLKaLTEAPDVEVDFRPTLNEEELKEIIGEYDALIVRSATKVTAAVLEKARRLKIIGR 71 79************889999************************************************* PP TIGR01327 69 aGvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtEly 137 aGvGvDNid++aat+kGi+v NaP gnt++aaE+++ l+l+laR+ip+a +++k++ W+rk+f+G+El+ lcl|NCBI__GCF_000024605.1:WP_012818167.1 72 AGVGVDNIDVKAATAKGIIVANAPGGNTVAAAEHTIGLMLSLARNIPEACARTKSGVWDRKSFMGVELR 140 ********************************************************************* PP TIGR01327 138 gktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltke 206 gk lG+iGlGriGsevakra+a++mk++ayDPyi+ee+a++l v+l ld+ll+eaD+it+H+Pl+ke lcl|NCBI__GCF_000024605.1:WP_012818167.1 141 GKVLGIIGLGRIGSEVAKRAQAMEMKIIAYDPYIPEERARDLRVKL-VPLDTLLQEADFITIHIPLSKE 208 *********************************************5.55******************** PP TIGR01327 207 tkgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvt 275 t +li++e++ kmK+gv+++NcaRGGi+dE+AL+eal+egkv++aalDvfekEP+t+++l++l+nvvvt lcl|NCBI__GCF_000024605.1:WP_012818167.1 209 TYHLIDREAFVKMKPGVRLINCARGGIVDEEALYEALKEGKVAGAALDVFEKEPVTSHPLFSLPNVVVT 277 ********************************************************************* PP TIGR01327 276 pHlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkea 344 pHlgAst Eaq +va +a+evl al+g +v++avNlp l e+l + p+l laeklG +a ql++++ lcl|NCBI__GCF_000024605.1:WP_012818167.1 278 PHLGASTVEAQLAVAEVIAQEVLTALRGGFVRHAVNLPYLRPEVLPVVGPFLPLAEKLGLFAAQLVSGR 346 ********************************************************************* PP TIGR01327 345 vkkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknlle 413 +++vev+++Ge+a+++++ll++a+lkg+l+ +l++++n+vnA+ vak+rgi+v+e+k+e +e+y nl++ lcl|NCBI__GCF_000024605.1:WP_012818167.1 347 INQVEVNYSGEIARYDTSLLNTAVLKGVLSVALQDTINYVNAPEVAKQRGIKVKETKQEREEEYVNLIS 415 ********************************************************************* PP TIGR01327 414 vkveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasm 482 vkvea +ge++vagt++ +kepr+veidg++vd peg++l+i + D+p +ig++g+l+g ++iNia+m lcl|NCBI__GCF_000024605.1:WP_012818167.1 416 VKVEAPEGEHTVAGTLVRGKEPRVVEIDGYRVDAVPEGYVLFIPHLDRPRIIGRIGTLIGAHDINIAAM 484 ********************************************************************* PP TIGR01327 483 qlgrkekggealmllslDeevseevleeikevpeiksvklv 523 q+grke gg+a+mlls+D++v+ee l+ei++v+++ +vk++ lcl|NCBI__GCF_000024605.1:WP_012818167.1 485 QVGRKEIGGKAIMLLSVDSPVPEETLREIAKVENVLDVKML 525 **************************************987 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: 0.01u 0.01s 00:00:00.02 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