Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_025273221.1 HALAL_RS0106475 phosphoserine transaminase
Query= BRENDA::P9WQ73 (376 letters) >NCBI__GCF_000527155.1:WP_025273221.1 Length = 372 Score = 409 bits (1050), Expect = e-119 Identities = 214/369 (57%), Positives = 262/369 (71%), Gaps = 5/369 (1%) Query: 9 LEIPTAIKPRDGRFGSGPSKVRLEQLQTLTTTAAALFGTSHRQAPVKNLVGRVRSGLAEL 68 + IP +KP DGRFGSGPSKV + L+ + + GTSHR+ VK V R++ GLAE Sbjct: 6 ITIPDELKPADGRFGSGPSKVPDTAMAALSASGHDIMGTSHRKPAVKGQVKRLQEGLAEF 65 Query: 69 FSLPDGYEVILGNGGATAFWDAAAFGLIDKRSLHLTYGEFSAKFASAVSKNPFVGEPIII 128 FSLPDGYEV+LG GG TAFWD ++GL+ +++ +GEF KF AVS P + P + Sbjct: 66 FSLPDGYEVVLGVGGTTAFWDVVSYGLVREQAQAAAFGEFGNKFVKAVSA-PHLRAPSVR 124 Query: 129 TSDPGSAPEPQTDPSVDVIAWAHNETSTGVAVAVRR-PEGSDDALVVIDATSGAGGLPVD 187 +PG+A + + VDV HNETSTGVAV V+R P+G DAL + DATS GLPVD Sbjct: 125 EGEPGNAAYLEAEAGVDVYGTTHNETSTGVAVPVQRVPDG--DALTIHDATSAVAGLPVD 182 Query: 188 IAETDAYYFAPQKNFASDGGLWLAIMSPAALSRIEAIAATGRWVPDFLSLPIAVENSLKN 247 + ETD YYFAPQK ASDGGLW+A+MSPAAL R I A+ R++P FL L AV+NS KN Sbjct: 183 MNETDCYYFAPQKGLASDGGLWIAVMSPAALERTAEIKASSRYIPAFLDLQTAVDNSRKN 242 Query: 248 QTYNTPAIATLALLAEQIDWLVGNGGLDWAVKRTADSSQRLYSWAQERPYTTPFVTDPGL 307 QTYNTPA+ATL L AEQID L GGL+ AVKR A S++ +YSWA+ P+VTDP L Sbjct: 243 QTYNTPAVATLILAAEQIDRLNATGGLEQAVKRCATSAETIYSWAEASRVAQPYVTDPDL 302 Query: 308 RSQVVGTIDFVDDVDAGTVAKILRANGIVDTEPYRKLGRNQLRVAMFPAVEPDDVSALTE 367 RS VV T+DF D VDA +A++LR NGIVDTEPYRKLGRNQLR+A +PAV+P DVS LT Sbjct: 303 RSSVVTTVDF-DGVDAADIAQVLRNNGIVDTEPYRKLGRNQLRIATYPAVDPADVSRLTG 361 Query: 368 CVDWVVERL 376 VD+VVERL Sbjct: 362 AVDYVVERL 370 Lambda K H 0.317 0.134 0.399 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: 474 Number of extensions: 16 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: 376 Length of database: 372 Length adjustment: 30 Effective length of query: 346 Effective length of database: 342 Effective search space: 118332 Effective search space used: 118332 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: 50 (23.9 bits)
Align candidate WP_025273221.1 HALAL_RS0106475 (phosphoserine transaminase)
to HMM TIGR01366 (putative phosphoserine aminotransferase (EC 2.6.1.52))
# 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/TIGR01366.hmm # target sequence database: /tmp/gapView.21866.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01366 [M=361] Accession: TIGR01366 Description: serC_3: putative phosphoserine aminotransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-160 518.6 2.2 5.5e-160 518.4 2.2 1.0 1 lcl|NCBI__GCF_000527155.1:WP_025273221.1 HALAL_RS0106475 phosphoserine tr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000527155.1:WP_025273221.1 HALAL_RS0106475 phosphoserine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 518.4 2.2 5.5e-160 5.5e-160 1 361 [] 13 370 .. 13 370 .. 0.99 Alignments for each domain: == domain 1 score: 518.4 bits; conditional E-value: 5.5e-160 TIGR01366 1 kpadgrfgagpskvrleqlqalvataasllgtshrqaavknlvgkvreglaelfslpdgyevilgngga 69 kpadgrfg+gpskv ++ al+a++ ++gtshr++avk v +++eglae+fslpdgyev+lg gg+ lcl|NCBI__GCF_000527155.1:WP_025273221.1 13 KPADGRFGSGPSKVPDTAMAALSASGHDIMGTSHRKPAVKGQVKRLQEGLAEFFSLPDGYEVVLGVGGT 81 7******************************************************************** PP TIGR01366 70 tafwdaatfgliekkslhlsfgefsskfakaaklapfldepeivtadpgsapeaqaeegvdvialahne 138 tafwd+ ++gl+ ++++ +fgef kf ka++ ap+l p + +pg+a +ae+gvdv++ +hne lcl|NCBI__GCF_000527155.1:WP_025273221.1 82 TAFWDVVSYGLVREQAQAAAFGEFGNKFVKAVS-APHLRAPSVREGEPGNAAYLEAEAGVDVYGTTHNE 149 *******************************97.8********************************** PP TIGR01366 139 tstgvavavrrpegsdealvvidatsgagglpvdiketdvyyfapqksfasdgglwlavlspaalerie 207 tstgvav+v+r+ +al + dats glpvd++etd yyfapqk +asdgglw+av+spaaler lcl|NCBI__GCF_000527155.1:WP_025273221.1 150 TSTGVAVPVQRVPDG-DALTIHDATSAVAGLPVDMNETDCYYFAPQKGLASDGGLWIAVMSPAALERTA 217 ***********9754.69*************************************************** PP TIGR01366 208 kiaasgrfvpeflslptavdnslknqtyntpavatlllldeqvdwlngnggldfavartkdsssrlysw 276 +i+as r++p fl+l+tavdns+knqtyntpavatl+l +eq+d ln+ ggl+ av+r + s++++ysw lcl|NCBI__GCF_000527155.1:WP_025273221.1 218 EIKASSRYIPAFLDLQTAVDNSRKNQTYNTPAVATLILAAEQIDRLNATGGLEQAVKRCATSAETIYSW 286 ********************************************************************* PP TIGR01366 277 aeereyatpfvadaakrsqvvgtidfsddidaavvakilrangivdtepyrklgrnqlrvamfpaidpa 345 ae+++ a p+v+d+ +rs vv t+df d +daa +a++lr ngivdtepyrklgrnqlr+a +pa+dpa lcl|NCBI__GCF_000527155.1:WP_025273221.1 287 AEASRVAQPYVTDPDLRSSVVTTVDF-DGVDAADIAQVLRNNGIVDTEPYRKLGRNQLRIATYPAVDPA 354 **************************.78**************************************** PP TIGR01366 346 dvealteavdfvvekl 361 dv++lt+avd+vve+l lcl|NCBI__GCF_000527155.1:WP_025273221.1 355 DVSRLTGAVDYVVERL 370 **************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (372 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.01 // [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