Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate Synpcc7942_1501 Synpcc7942_1501 D-3-phosphoglycerate dehydrogenase
Query= uniprot:Q6LWW6 (523 letters) >FitnessBrowser__SynE:Synpcc7942_1501 Length = 546 Score = 432 bits (1111), Expect = e-125 Identities = 237/528 (44%), Positives = 347/528 (65%), Gaps = 8/528 (1%) Query: 1 MSKILITDPLHESAVEILKQAGEVEVATGLTVEELKLKIKDVDALVIRSGTTATREIIEA 60 M K+L++DP+ + ++IL Q +V+V TGL+ EL I + DAL++RSGT T E+IEA Sbjct: 18 MPKVLVSDPIDQVGLDILSQVAQVDVKTGLSPSELAQIIGEYDALMLRSGTRVTAEVIEA 77 Query: 61 SENLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAAARNIPQATA 120 + L++I RAGVGVDNVD+ AAT +GIVVVN+P+ ++I+ AE MML+ +R+IP A A Sbjct: 78 GQKLRIIGRAGVGVDNVDVPAATRRGIVVVNSPEGNTIAAAEHTLAMMLSLSRHIPDANA 137 Query: 121 SIKSGKWDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVASEL 180 S KSG WDRKSF G E+Y KTLG+VGLG+IG VA A+A GM ++AYDP+I + A ++ Sbjct: 138 STKSGGWDRKSFVGTEVYKKTLGVVGLGKIGSHVATVAKAMGMKLLAYDPFISAERAEQI 197 Query: 181 GIKLLTVDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNCARGGLIDEAALY 240 G +L+ +D L +D+ITLH+P TP+T ++I E +A MK I+NCARGG+I+E AL Sbjct: 198 GARLVELDILFQEADYITLHIPKTPETANLINAETLAKMKPTTRIINCARGGVINEQALA 257 Query: 241 DALNSGKIKAAALDVFEQEP-PKESPLLTL-NNLIGTPHQGASTEEAQLSAGTIVAEQTV 298 DA+ +GKI AALDV++QEP +SPL L NLI TPH GAST EAQ++ VAEQ Sbjct: 258 DAIAAGKIGGAALDVYDQEPLQADSPLRALGKNLILTPHLGASTTEAQVNVAVDVAEQIR 317 Query: 299 KILKGESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMGGLAK 358 +L G A + VN+P + + ++KL+PY+ LAE +G++ Q +E L + G LA Sbjct: 318 DVLLGLPARSAVNIPGLYPDILEKLRPYLQLAETLGNLLSQVAGGRLEQLTVRLQGELAA 377 Query: 359 EKTEILKRSFLKGILAPILLAGVNLVNAPVIAKSRNIKIAEGTMSES---DY-GNSIKIS 414 ++++ + + LKG+L L VN VNA + AK R I+I E T ES DY G S+++ Sbjct: 378 QQSQPIVVAALKGLLTQALRERVNYVNAMIEAKERGIRIIE-TRDESVRDDYAGGSLQLV 436 Query: 415 AKGENDEISIIGS-IEHNEVVFREINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEH 473 A G N E ++G+ + E+ ++ + +++ P + +H D PG++GK+G LLG Sbjct: 437 ATGSNGEHRVMGALLGDGEIRITNVDEFPVNVPPSRYMLFTRHRDMPGIIGKIGSLLGSF 496 Query: 474 GINIAGMQVGRREPGGHSIMFLDIDHMISDEVLDEIRKMENVRAAKSI 521 +NIA MQVGRR G ++M L +D + + +L EI K+ + A ++ Sbjct: 497 NVNIASMQVGRRIVRGDAVMVLSLDDPLPEGILAEITKVAGISDAYTV 544 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: 694 Number of extensions: 28 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: 546 Length adjustment: 35 Effective length of query: 488 Effective length of database: 511 Effective search space: 249368 Effective search space used: 249368 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 Synpcc7942_1501 Synpcc7942_1501 (D-3-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.16054.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-216 703.7 2.8 9.1e-216 703.6 2.8 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_1501 Synpcc7942_1501 D-3-phosphoglyce Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_1501 Synpcc7942_1501 D-3-phosphoglycerate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 703.6 2.8 9.1e-216 9.1e-216 1 525 [] 20 546 .] 20 546 .] 0.98 Alignments for each domain: == domain 1 score: 703.6 bits; conditional E-value: 9.1e-216 TIGR01327 1 kvlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRa 69 kvlv+d++++ g+++l++ + +vdvktgls el ++i +ydal++RS t+vt+e++ea +kL++igRa lcl|FitnessBrowser__SynE:Synpcc7942_1501 20 KVLVSDPIDQVGLDILSQVA-QVDVKTGLSPSELAQIIGEYDALMLRSGTRVTAEVIEAGQKLRIIGRA 87 7****************996.************************************************ PP TIGR01327 70 GvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElyg 138 GvGvDN+d++aat++Gi+vvN+Pegnti+aaE++la++l+l+R+ip+a++s+k++ W+rk+f+GtE+y+ lcl|FitnessBrowser__SynE:Synpcc7942_1501 88 GVGVDNVDVPAATRRGIVVVNSPEGNTIAAAEHTLAMMLSLSRHIPDANASTKSGGWDRKSFVGTEVYK 156 ********************************************************************* PP TIGR01327 139 ktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltket 207 ktlGv+GlG+iGs+va+ aka+gmk+layDP+is e+ae++g +l +ld l++eaD it+H+P+t+et lcl|FitnessBrowser__SynE:Synpcc7942_1501 157 KTLGVVGLGKIGSHVATVAKAMGMKLLAYDPFISAERAEQIGARL-VELDILFQEADYITLHIPKTPET 224 ********************************************5.55********************* PP TIGR01327 208 kgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPpt.dnklleldn.vvv 274 ++li++e+lakmK++ +i+NcaRGG+i+E+AL++a+ +gk+ +aalDv+ +EP + d++l +l + +++ lcl|FitnessBrowser__SynE:Synpcc7942_1501 225 ANLINAETLAKMKPTTRIINCARGGVINEQALADAIAAGKIGGAALDVYDQEPLQaDSPLRALGKnLIL 293 *****************************************************9989***987544*** PP TIGR01327 275 tpHlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllke 343 tpHlgAst+Eaq nvav+vae+++++l g +++savN+p l + lekl+pyl+lae+lG+l sq++++ lcl|FitnessBrowser__SynE:Synpcc7942_1501 294 TPHLGASTTEAQVNVAVDVAEQIRDVLLGLPARSAVNIPGLYPDILEKLRPYLQLAETLGNLLSQVAGG 362 ********************************************************************* PP TIGR01327 344 avkkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeese.dyk.n 410 + ++++v l+Gela+++s++++ a+lkgll ++l+e+vn+vnA++ akergi++ e+++e+++ dy lcl|FitnessBrowser__SynE:Synpcc7942_1501 363 RLEQLTVRLQGELAAQQSQPIVVAALKGLLTQALRERVNYVNAMIEAKERGIRIIETRDESVRdDYAgG 431 ******************************************************999998875268636 PP TIGR01327 411 llevkveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNi 479 +l++ +++++ge+ v g++l++ e ri+++d+f v++ p+ ++l+++++D+pG+igk+gsllg++++Ni lcl|FitnessBrowser__SynE:Synpcc7942_1501 432 SLQLVATGSNGEHRVMGALLGDGEIRITNVDEFPVNVPPSRYMLFTRHRDMPGIIGKIGSLLGSFNVNI 500 9******************************************************************** PP TIGR01327 480 asmqlgrkekggealmllslDeevseevleeikevpeiksvklvel 525 asmq+gr+ +g+a+m+lslD++++e++l+ei++v+ i ++++v l lcl|FitnessBrowser__SynE:Synpcc7942_1501 501 ASMQVGRRIVRGDAVMVLSLDDPLPEGILAEITKVAGISDAYTVVL 546 *****************************************99976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (525 nodes) Target sequences: 1 (546 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: 00:00:00.03 # Mc/sec: 8.25 // [ok]
This GapMind analysis is from Apr 09 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