Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_037573661.1 BS73_RS17765 phosphoserine transaminase
Query= BRENDA::P9WQ73 (376 letters) >NCBI__GCF_000744815.1:WP_037573661.1 Length = 372 Score = 520 bits (1340), Expect = e-152 Identities = 251/369 (68%), Positives = 297/369 (80%), Gaps = 1/369 (0%) Query: 9 LEIPTAIKPRDGRFGSGPSKVRLEQLQTLTTTAAALFGTSHRQAPVKNLVGRVRSGLAEL 68 +EIP+ +KP DGRFG+GPSKVR E L L T +L GTSHRQAPVKNLV RVR G+A+L Sbjct: 4 IEIPSDLKPADGRFGAGPSKVRPEALNALAATGTSLLGTSHRQAPVKNLVRRVREGVAQL 63 Query: 69 FSLPDGYEVILGNGGATAFWDAAAFGLIDKRSLHLTYGEFSAKFASAVSKNPFVGEPIII 128 FSLP+GY+V+LGNGG+TAFWD AA GL+ ++S HL++GEFS+KFA A P++ +P II Sbjct: 64 FSLPEGYQVVLGNGGSTAFWDVAAHGLVRRKSQHLSFGEFSSKFAKATKTAPWLADPTII 123 Query: 129 TSDPGSAPEPQTDPSVDVIAWAHNETSTGVAVAVRRPEGSD-DALVVIDATSGAGGLPVD 187 TSDPG+ PE + VDV A+ HNETSTGVA+ + R G+D DALV++DATSGAGGLPVD Sbjct: 124 TSDPGTHPEAAAEAGVDVYAFTHNETSTGVAMPINRVAGADEDALVLVDATSGAGGLPVD 183 Query: 188 IAETDAYYFAPQKNFASDGGLWLAIMSPAALSRIEAIAATGRWVPDFLSLPIAVENSLKN 247 I +TD YYFAPQKNFASDGGLW+ SPAAL R IAA R++P F LP A++NS K+ Sbjct: 184 ITQTDVYYFAPQKNFASDGGLWIGAFSPAALDRAAEIAAGDRYIPAFFDLPTAIDNSAKD 243 Query: 248 QTYNTPAIATLALLAEQIDWLVGNGGLDWAVKRTADSSQRLYSWAQERPYTTPFVTDPGL 307 QTYNTP++ATL LLA+Q+DWL GNGGLDWA RTADSS RLY WA++ YTTPFVTDP Sbjct: 244 QTYNTPSVATLFLLADQLDWLNGNGGLDWATARTADSSSRLYGWAEKTAYTTPFVTDPAK 303 Query: 308 RSQVVGTIDFVDDVDAGTVAKILRANGIVDTEPYRKLGRNQLRVAMFPAVEPDDVSALTE 367 RSQV+GTIDF D VDA VAK+LRANGIVDTEPYRKLGRNQLRVAMF A++P DV ALT Sbjct: 304 RSQVIGTIDFADSVDAAAVAKVLRANGIVDTEPYRKLGRNQLRVAMFAAIDPADVEALTA 363 Query: 368 CVDWVVERL 376 C+D VVERL Sbjct: 364 CIDHVVERL 372 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: 523 Number of extensions: 14 Number of successful extensions: 2 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_037573661.1 BS73_RS17765 (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.3295256.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-209 681.8 3.1 1.3e-209 681.6 3.1 1.0 1 NCBI__GCF_000744815.1:WP_037573661.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000744815.1:WP_037573661.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 681.6 3.1 1.3e-209 1.3e-209 1 361 [] 11 372 .] 11 372 .] 1.00 Alignments for each domain: == domain 1 score: 681.6 bits; conditional E-value: 1.3e-209 TIGR01366 1 kpadgrfgagpskvrleqlqalvataasllgtshrqaavknlvgkvreglaelfslpdgyevilgnggatafw 73 kpadgrfgagpskvr+e+l+al+at++sllgtshrqa+vknlv +vreg+a+lfslp+gy+v+lgngg+tafw NCBI__GCF_000744815.1:WP_037573661.1 11 KPADGRFGAGPSKVRPEALNALAATGTSLLGTSHRQAPVKNLVRRVREGVAQLFSLPEGYQVVLGNGGSTAFW 83 7************************************************************************ PP TIGR01366 74 daatfgliekkslhlsfgefsskfakaaklapfldepeivtadpgsapeaqaeegvdvialahnetstgvava 146 d+a++gl+ +ks+hlsfgefsskfaka+k ap+l++p+i+t+dpg++pea ae+gvdv+a++hnetstgva++ NCBI__GCF_000744815.1:WP_037573661.1 84 DVAAHGLVRRKSQHLSFGEFSSKFAKATKTAPWLADPTIITSDPGTHPEAAAEAGVDVYAFTHNETSTGVAMP 156 ************************************************************************* PP TIGR01366 147 vrrpegsde.alvvidatsgagglpvdiketdvyyfapqksfasdgglwlavlspaaleriekiaasgrfvpe 218 + r++g+de alv++datsgagglpvdi++tdvyyfapqk+fasdgglw++++spaal+r+ +iaa +r++p NCBI__GCF_000744815.1:WP_037573661.1 157 INRVAGADEdALVLVDATSGAGGLPVDITQTDVYYFAPQKNFASDGGLWIGAFSPAALDRAAEIAAGDRYIPA 229 *******988*************************************************************** PP TIGR01366 219 flslptavdnslknqtyntpavatlllldeqvdwlngnggldfavartkdsssrlyswaeereyatpfvadaa 291 f++lpta+dns k+qtyntp+vatl+ll++q+dwlngnggld+a+art+dsssrly wae++ y+tpfv+d+a NCBI__GCF_000744815.1:WP_037573661.1 230 FFDLPTAIDNSAKDQTYNTPSVATLFLLADQLDWLNGNGGLDWATARTADSSSRLYGWAEKTAYTTPFVTDPA 302 ************************************************************************* PP TIGR01366 292 krsqvvgtidfsddidaavvakilrangivdtepyrklgrnqlrvamfpaidpadvealteavdfvvekl 361 krsqv+gtidf+d++daa+vak+lrangivdtepyrklgrnqlrvamf aidpadvealt ++d+vve+l NCBI__GCF_000744815.1:WP_037573661.1 303 KRSQVIGTIDFADSVDAAAVAKVLRANGIVDTEPYRKLGRNQLRVAMFAAIDPADVEALTACIDHVVERL 372 ********************************************************************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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 12.53 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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