Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate WP_012966581.1 FERP_RS10600 phosphoglycerate dehydrogenase
Query= uniprot:Q6LWW6 (523 letters) >NCBI__GCF_000025505.1:WP_012966581.1 Length = 527 Score = 476 bits (1224), Expect = e-138 Identities = 253/519 (48%), Positives = 355/519 (68%), Gaps = 7/519 (1%) Query: 3 KILITDPLHESAVEILKQAG-EVEVATGLTVEELKLKIKDVDALVIRSGTTATREIIEAS 61 K+L+ + + A+E+LK G EV+V ++ EELK IKD DAL++RS TREIIE Sbjct: 2 KVLVASNIAKEAIELLKAEGMEVDVRADISEEELKEVIKDYDALIVRSKPKVTREIIERG 61 Query: 62 ENLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAAARNIPQATAS 121 E LK+I RAGVGVDN+D+DAATE+GI+VVNAP ++IS AEL G++++AAR IPQA S Sbjct: 62 EKLKIIGRAGVGVDNIDVDAATERGIIVVNAPGGNTISTAELTMGLIISAARKIPQADRS 121 Query: 122 IKSGKWDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVASELG 181 +K GKW+RK F+G+E+ GKTLGI+GLGRIG +VAKRA++F M ++AYDPYI + A +G Sbjct: 122 VKEGKWERKKFEGLELRGKTLGIIGLGRIGFEVAKRAKSFEMRVIAYDPYISPERAKSIG 181 Query: 182 IKLLTVDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNCARGGLIDEAALYD 241 ++L++ D L SD IT+HVP T +T+ MI E+ MK N++I+NCARGG++DE ALY+ Sbjct: 182 VELVSFDYLIENSDIITVHVPKTKETEKMISYEEFRKMKDNVIIVNCARGGIVDEDALYE 241 Query: 242 ALNSGKIKAAALDVFEQEPPK-ESPLLTLNNLIGTPHQGASTEEAQLSAGTIVAEQTVKI 300 AL SGK+ AALDV+E+EPP PL L N+I TPH GAST+EAQ S G I+A + + Sbjct: 242 ALKSGKVYMAALDVYEKEPPNFNHPLFKLENVITTPHIGASTKEAQKSVGMIIARDIINL 301 Query: 301 LKGESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMGGLAKEK 360 KG N VNLP + E + L PY+ LAEKMG +A L + + ++ITY G LA + Sbjct: 302 YKGLPVINAVNLPSLKPEDFEYLMPYITLAEKMGKIASARLGGNFKEVKITYRGKLANKD 361 Query: 361 TEILKRSFLKGILAPILLAGVNLVNAPVIAKSRNIKIAEGTMSESD-YGNSIKISAKGEN 419 T + R+ LKG+L IL A +NLV++ IAK R I+I E + +D Y + +++ KGE Sbjct: 362 TAYVARALLKGLLETILGANINLVSSMPIAKQRGIRIEESRIESTDSYESLLEVEVKGEK 421 Query: 420 DEISIIG-SIEHNEVVFREINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEHGINIA 478 IS+ G S ++ I+ Y++D P G I H D+PG++G+VG L G++ INIA Sbjct: 422 -SISLAGTSFGRDDYRIIRIDRYKVDFVPRGHYIISLHEDKPGVIGRVGTLFGQYNINIA 480 Query: 479 GMQVGR--REPGGHSIMFLDIDHMISDEVLDEIRKMENV 515 GM VGR +PGG +M L +D ++EVL+++ K++ + Sbjct: 481 GMIVGRYGDKPGGVQLMLLLVDDPPTEEVLEKMVKLDGI 519 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: 738 Number of extensions: 51 Number of successful extensions: 7 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_012966581.1 FERP_RS10600 (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.24926.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-221 720.7 2.8 6.3e-221 720.6 2.8 1.0 1 lcl|NCBI__GCF_000025505.1:WP_012966581.1 FERP_RS10600 phosphoglycerate de Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025505.1:WP_012966581.1 FERP_RS10600 phosphoglycerate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 720.6 2.8 6.3e-221 6.3e-221 1 524 [. 2 526 .. 2 527 .] 0.99 Alignments for each domain: == domain 1 score: 720.6 bits; conditional E-value: 6.3e-221 TIGR01327 1 kvlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRa 69 kvlva ++++e+iellk +++evdv+ ++s+eel e+ikdydalivRS+ kvt+e++e+ ekLk+igRa lcl|NCBI__GCF_000025505.1:WP_012966581.1 2 KVLVASNIAKEAIELLKAEGMEVDVRADISEEELKEVIKDYDALIVRSKPKVTREIIERGEKLKIIGRA 70 79******************************************************************* PP TIGR01327 70 GvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElyg 138 GvGvDNid++aat++Gi+vvNaP gntis+aEl++ l++++aRkipqad+svke+kWerkkf G+El+g lcl|NCBI__GCF_000025505.1:WP_012966581.1 71 GVGVDNIDVDAATERGIIVVNAPGGNTISTAELTMGLIISAARKIPQADRSVKEGKWERKKFEGLELRG 139 ********************************************************************* PP TIGR01327 139 ktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltket 207 ktlG+iGlGriG evakrak+++m+v+ayDPyis+e+a+++gve l ++d l++++D+itvHvP+tket lcl|NCBI__GCF_000025505.1:WP_012966581.1 140 KTLGIIGLGRIGFEVAKRAKSFEMRVIAYDPYISPERAKSIGVE-LVSFDYLIENSDIITVHVPKTKET 207 ********************************************.556********************* PP TIGR01327 208 kgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPpt.dnklleldnvvvt 275 +++i+ ee+ kmK++viivNcaRGGi+dE+AL+eal++gkv +aalDv+ekEPp+ +++l++l+nv++t lcl|NCBI__GCF_000025505.1:WP_012966581.1 208 EKMISYEEFRKMKDNVIIVNCARGGIVDEDALYEALKSGKVYMAALDVYEKEPPNfNHPLFKLENVITT 276 ******************************************************98999********** PP TIGR01327 276 pHlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkea 344 pH+gAst+Eaq+ v++++a +++++ kg +v +avNlp+l+ e++e l+py++laek+Gk+as l+++ lcl|NCBI__GCF_000025505.1:WP_012966581.1 277 PHIGASTKEAQKSVGMIIARDIINLYKGLPVINAVNLPSLKPEDFEYLMPYITLAEKMGKIASARLGGN 345 ********************************************************************* PP TIGR01327 345 vkkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknlle 413 k+v++t++G+la++++ + +allkgll+ +l +++nlv+ + +ak+rgi++ees+ e++++y++lle lcl|NCBI__GCF_000025505.1:WP_012966581.1 346 FKEVKITYRGKLANKDTAYVARALLKGLLETILGANINLVSSMPIAKQRGIRIEESRIESTDSYESLLE 414 ********************************************************************* PP TIGR01327 414 vkveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasm 482 v+v+++k ++s+agt ++ + +ri++id+++vd+ p+g+++i+ ++DkpGvig+vg+l+g+++iNia+m lcl|NCBI__GCF_000025505.1:WP_012966581.1 415 VEVKGEK-SISLAGTSFGRDDYRIIRIDRYKVDFVPRGHYIISLHEDKPGVIGRVGTLFGQYNINIAGM 482 ****975.799********************************************************** PP TIGR01327 483 qlgrk..ekggealmllslDeevseevleeikevpeiksvklve 524 +gr + gg +lmll +D++++eevle++ +++ i +++++ lcl|NCBI__GCF_000025505.1:WP_012966581.1 483 IVGRYgdKPGGVQLMLLLVDDPPTEEVLEKMVKLDGIIDATYIY 526 ****755999******************************9986 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: 9.43 // [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