Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_028485474.1 A377_RS0110550 3-phosphoserine/phosphohydroxythreonine transaminase
Query= BRENDA::P23721 (362 letters) >NCBI__GCF_000384235.1:WP_028485474.1 Length = 354 Score = 383 bits (984), Expect = e-111 Identities = 197/358 (55%), Positives = 245/358 (68%), Gaps = 9/358 (2%) Query: 5 FNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNVP 64 FNFS+GPAMLP V+++AQ E DW G SVME+SHR EF+ VA E E D R+L+ +P Sbjct: 4 FNFSAGPAMLPEAVMQEAQAEFLDWQNTGMSVMEMSHRSPEFMSVAHEMEADLRELMAIP 63 Query: 65 SNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPN-VFDAKV 123 +YKVLF HGG QFA +P N+ T DY + G W+A AIKEA ++ N V A+ Sbjct: 64 DDYKVLFTHGGASLQFAGIPFNLTQPGDTVDYCNTGVWSAKAIKEASRFVQVNEVAKAET 123 Query: 124 TVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSRP 183 T+ +WQLSDNA Y+H C NETI G+ PD D + ADFSSTILSRP Sbjct: 124 TIPDFD------QWQLSDNAKYLHICQNETITGVEFQSLPD--TDKPIIADFSSTILSRP 175 Query: 184 IDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPT 243 I+V+ YG+IYAGAQKNIGPAGL IVIVREDL+G A P+++++ + SMFNTP T Sbjct: 176 INVADYGLIYAGAQKNIGPAGLAIVIVREDLIGHARETTPTLMNWQTYDQFESMFNTPAT 235 Query: 244 FAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVPFQ 303 FAWYL+G VFKWLKA GG+ M +N++KA+ LY +ID S Y N+VA + RS MNV F+ Sbjct: 236 FAWYLAGKVFKWLKAQGGLDAMATLNERKAQKLYTLIDRSGLYYNEVAPSVRSWMNVTFK 295 Query: 304 LADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRH 361 L D L++ FL ES AGL +L+GH+ GGMRASIYNAMP GV AL DFM FE+RH Sbjct: 296 LKDETLNQAFLTESREAGLLSLRGHKTYGGMRASIYNAMPEAGVDALVDFMQAFEQRH 353 Lambda K H 0.319 0.136 0.405 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: 394 Number of extensions: 20 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: 362 Length of database: 354 Length adjustment: 29 Effective length of query: 333 Effective length of database: 325 Effective search space: 108225 Effective search space used: 108225 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
Align candidate WP_028485474.1 A377_RS0110550 (3-phosphoserine/phosphohydroxythreonine transaminase)
to HMM TIGR01364 (serC: phosphoserine transaminase (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/TIGR01364.hmm # target sequence database: /tmp/gapView.10230.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01364 [M=358] Accession: TIGR01364 Description: serC_1: phosphoserine transaminase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-152 493.0 0.0 2.4e-152 492.9 0.0 1.0 1 lcl|NCBI__GCF_000384235.1:WP_028485474.1 A377_RS0110550 3-phosphoserine/p Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384235.1:WP_028485474.1 A377_RS0110550 3-phosphoserine/phosphohydroxythreonine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 492.9 0.0 2.4e-152 2.4e-152 2 358 .] 4 353 .. 3 353 .. 0.98 Alignments for each domain: == domain 1 score: 492.9 bits; conditional E-value: 2.4e-152 TIGR01364 2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflq 70 +nFsaGPa+lpe+v+++aq+e+ld++++g+svme+sHRs ef++v++e e dlreL+ ipd+y+vlf lcl|NCBI__GCF_000384235.1:WP_028485474.1 4 FNFSAGPAMLPEAVMQEAQAEFLDWQNTGMSVMEMSHRSPEFMSVAHEMEADLRELMAIPDDYKVLFTH 72 8******************************************************************** PP TIGR01364 71 GGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelked 139 GGa+ qfa +p+nl++ ++++dy +tG+ws+ka+kea+++++ v+ va++e ++ipd ++++l+++ lcl|NCBI__GCF_000384235.1:WP_028485474.1 73 GGASLQFAGIPFNLTQPGDTVDYCNTGVWSAKAIKEASRFVQ-VNEVAKAE----TTIPDFDQWQLSDN 136 ****************************************98.88888885....78************ PP TIGR01364 140 aayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrk 208 a+y+++c+neti+Gvef++lp +++p++aD+ss ilsr+i+v++ygliyaGaqKniGpaG+++vivr+ lcl|NCBI__GCF_000384235.1:WP_028485474.1 137 AKYLHICQNETITGVEFQSLP-DTDKPIIADFSSTILSRPINVADYGLIYAGAQKNIGPAGLAIVIVRE 204 *********************.77899****************************************** PP TIGR01364 209 dllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaid 277 dl+++a++++p+++++++ + +s++ntp+tfa+y++g+v+kwlk++GG+++++ n++Ka+ lY +id lcl|NCBI__GCF_000384235.1:WP_028485474.1 205 DLIGHARETTPTLMNWQTYDQFESMFNTPATFAWYLAGKVFKWLKAQGGLDAMATLNERKAQKLYTLID 273 ********************************************************************* PP TIGR01364 278 esegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqa 346 +s g+y n+v+++ Rs+mnv+F+lk+e l++ Fl+e++e+gl+sl+Gh++ GG+RasiYna+p ++v a lcl|NCBI__GCF_000384235.1:WP_028485474.1 274 RS-GLYYNEVAPSVRSWMNVTFKLKDETLNQAFLTESREAGLLSLRGHKTYGGMRASIYNAMPEAGVDA 341 99.6999************************************************************** PP TIGR01364 347 LvdfmkeFekkh 358 Lvdfm+ Fe++h lcl|NCBI__GCF_000384235.1:WP_028485474.1 342 LVDFMQAFEQRH 353 *********987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (358 nodes) Target sequences: 1 (354 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: 00:00:00.01 # Mc/sec: 7.61 // [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