Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate WP_093395386.1 BM091_RS09805 phosphoglycerate dehydrogenase
Query= uniprot:Q6LWW6 (523 letters) >NCBI__GCF_900114975.1:WP_093395386.1 Length = 528 Score = 427 bits (1098), Expect = e-124 Identities = 226/520 (43%), Positives = 332/520 (63%), Gaps = 5/520 (0%) Query: 1 MSKILITDPLHESAVEILKQAGE--VEVATGLTVEELKLKIKDVDALVIRSGTTATREII 58 M KIL++DPL E+ +E L E VEV T LT EEL+ +K+ DALVIRS T TR++I Sbjct: 1 MYKILVSDPLAEAGIEKLMSVPEFEVEVNTSLTHEELREVVKECDALVIRSSTKVTRDVI 60 Query: 59 EASENLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAAARNIPQA 118 EA + LKVIARAG+G+DNVD+DAAT KGIVV+N P+ + I+ AE ++LA +RNIPQA Sbjct: 61 EAGDRLKVIARAGIGLDNVDIDAATRKGIVVMNTPEGNVITTAEHTIALLLAVSRNIPQA 120 Query: 119 TASIKSGKWDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVAS 178 AS+K+GKW++K F+G E++ K LGI+G+GRIG+ VA RA+ M ++AYDPYI DV Sbjct: 121 DASLKAGKWEKKKFRGKEVFNKVLGIIGVGRIGRVVADRAKGLKMQVIAYDPYISSDVVE 180 Query: 179 ELGIKLLTVDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNCARGGLIDEAA 238 LGI+ +++DEL SD+IT+H PLT +T++++ K+ MK + I+NCARGG+++E Sbjct: 181 RLGIEAVSLDELLARSDYITVHTPLTQETRNLLNKDAFKKMKKGVFIINCARGGIVNEED 240 Query: 239 LYDALNSGKIKAAALDVFEQE-PPKESPLLTLNNLIGTPHQGASTEEAQLSAGTIVAEQT 297 L +A+ G + AA+DVF E PP + PLL L ++ TPH GAST+EAQ + VA+Q Sbjct: 241 LAEAIKEGIVAGAAIDVFTVEPPPPDHPLLNLEKVVLTPHLGASTDEAQENVAIAVADQV 300 Query: 298 VKILKGESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMGGLA 357 + L + N +N P + E + L+PY+ L+EK+G + Q + + I Y+G + Sbjct: 301 IDYLLKGTIRNAINAPTIDGEVLANLRPYLTLSEKLGCLVSQITRGAPVEIGIEYVGDVT 360 Query: 358 KEKTEILKRSFLKGILAPILLAGVNLVNAPVIAKSRNIKIAEGTMSES-DYGNSIKISAK 416 + L S +KG+L+ + VN VNA +A+ RNI I E T E+ D+ N + + K Sbjct: 361 DLDRQPLTISIVKGLLSTYMGDEVNFVNAVALARERNISIRETTRGEAEDFTNLVIVRLK 420 Query: 417 GENDEISIIGSI-EHNEVVFREINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEHGI 475 DE + G+I + IN +R++ + EG + +I +ID PG +G +G LG H I Sbjct: 421 TSEDENIVAGTIFGKRDARLVRINDFRLEAEMEGNLLLIYNIDTPGTIGAIGTCLGNHNI 480 Query: 476 NIAGMQVGRREPGGHSIMFLDIDHMISDEVLDEIRKMENV 515 NI+ M VG+ G +I+ L D + D V+ E+ ++NV Sbjct: 481 NISMMDVGQVLEKGQNIILLRTDTPVPDHVIKELLSLKNV 520 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: 703 Number of extensions: 32 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: 528 Length adjustment: 35 Effective length of query: 488 Effective length of database: 493 Effective search space: 240584 Effective search space used: 240584 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_093395386.1 BM091_RS09805 (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.1960.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-204 667.0 10.2 1.2e-204 666.9 10.2 1.0 1 lcl|NCBI__GCF_900114975.1:WP_093395386.1 BM091_RS09805 phosphoglycerate d Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900114975.1:WP_093395386.1 BM091_RS09805 phosphoglycerate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 666.9 10.2 1.2e-204 1.2e-204 1 522 [. 3 525 .. 3 528 .] 0.99 Alignments for each domain: == domain 1 score: 666.9 bits; conditional E-value: 1.2e-204 TIGR01327 1 kvlvadklseegie.llkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigR 68 k+lv+d+l+e+gie l++ e+ev+v+t l++eel e++k+ dal++RS+tkvt++++ea ++Lkvi+R lcl|NCBI__GCF_900114975.1:WP_093395386.1 3 KILVSDPLAEAGIEkLMSVPEFEVEVNTSLTHEELREVVKECDALVIRSSTKVTRDVIEAGDRLKVIAR 71 79************99999************************************************** PP TIGR01327 69 aGvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtEly 137 aG+G+DN+di+aat+kGi+v+N+Pegn i++aE+++allla++R+ipqad+s+k++kWe+kkf G E++ lcl|NCBI__GCF_900114975.1:WP_093395386.1 72 AGIGLDNVDIDAATRKGIVVMNTPEGNVITTAEHTIALLLAVSRNIPQADASLKAGKWEKKKFRGKEVF 140 ********************************************************************* PP TIGR01327 138 gktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltke 206 +k lG+iG+GriG va+rak+l+m+v+ayDPyis++ +e+lg+e + +ldella++D itvH+Plt+e lcl|NCBI__GCF_900114975.1:WP_093395386.1 141 NKVLGIIGVGRIGRVVADRAKGLKMQVIAYDPYISSDVVERLGIE-AVSLDELLARSDYITVHTPLTQE 208 *********************************************.666******************** PP TIGR01327 207 tkgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPpt.dnklleldnvvv 274 t++l++k++++kmKkgv i+NcaRGGi++E+ L+ea++eg v++aa+Dvf+ EPp d++ll+l++vv+ lcl|NCBI__GCF_900114975.1:WP_093395386.1 209 TRNLLNKDAFKKMKKGVFIINCARGGIVNEEDLAEAIKEGIVAGAAIDVFTVEPPPpDHPLLNLEKVVL 277 *****************************************************9887************ PP TIGR01327 275 tpHlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllke 343 tpHlgAst Eaqenva+ va++v+++l + ++a+N+p++d e+l++l+pyl+l+eklG l+sq++ + lcl|NCBI__GCF_900114975.1:WP_093395386.1 278 TPHLGASTDEAQENVAIAVADQVIDYLLKGTIRNAINAPTIDGEVLANLRPYLTLSEKLGCLVSQITRG 346 ********************************************************************* PP TIGR01327 344 avkkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknll 412 a+ ++ +++ G++++ + ++lt +++kgll+ + +evn+vnA a+a+er+i+++e+++ e+ed++nl+ lcl|NCBI__GCF_900114975.1:WP_093395386.1 347 APVEIGIEYVGDVTDLDRQPLTISIVKGLLSTYMGDEVNFVNAVALARERNISIRETTRGEAEDFTNLV 415 ********************************************************************* PP TIGR01327 413 evkveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNias 481 v+++++++e vagt++++ r+v+i++f+++ e eg ll+i+n D+pG+ig +g+ lg+++iNi lcl|NCBI__GCF_900114975.1:WP_093395386.1 416 IVRLKTSEDENIVAGTIFGKRDARLVRINDFRLEAEMEGNLLLIYNIDTPGTIGAIGTCLGNHNINISM 484 ********************************************************************* PP TIGR01327 482 mqlgrkekggealmllslDeevseevleeikevpeiksvkl 522 m +g+ ++g+ ++ll+ D +v+++v++e+ ++++++ v+ lcl|NCBI__GCF_900114975.1:WP_093395386.1 485 MDVGQVLEKGQNIILLRTDTPVPDHVIKELLSLKNVEYVQR 525 *******************************9999988875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (525 nodes) Target sequences: 1 (528 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: 12.30 // [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