Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_012536419.1 AFE_RS04200 3-phosphoserine/phosphohydroxythreonine aminotransferase
Query= BRENDA::P23721 (362 letters) >NCBI__GCF_000021485.1:WP_012536419.1 Length = 362 Score = 384 bits (985), Expect = e-111 Identities = 201/361 (55%), Positives = 256/361 (70%), Gaps = 5/361 (1%) Query: 4 IFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNV 63 IFNFS+GPA+LP VL+Q Q EL DW+G G SVME+SHRG EF+++A EAE+D RDLL++ Sbjct: 5 IFNFSAGPAVLPHVVLEQVQAELLDWHGSGMSVMEMSHRGPEFMKIAAEAEQDLRDLLDI 64 Query: 64 PSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKV 123 P+NYK+LF GG QFA VPLN++ A YV G W+ AI EA+++ + A Sbjct: 65 PANYKILFLQGGATLQFAMVPLNLMRGHGKASYVQTGIWSKKAIAEARRFTAVEI--AAS 122 Query: 124 TVDGLRAVKPMR-EWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSR 182 D + PM+ +WQ+S + AY+H NETI G+ D PD G D+ + +D SS ILS+ Sbjct: 123 NEDRHASYVPMQADWQVSPDTAYVHITGNETIGGVEFDFIPDLG-DIPLVSDASSHILSK 181 Query: 183 PIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPP 242 P DVSR+G+IYAGAQKNIGPAGLT+VIVR+DLLG A ++LDY++ SM NTPP Sbjct: 182 PTDVSRFGLIYAGAQKNIGPAGLTLVIVRDDLLGHAPANTATMLDYAVYAKEESMHNTPP 241 Query: 243 TFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNS-DFYRNDVAKANRSRMNVP 301 TFA Y++GLVFKWLK GG+ M +IN +KA LLY ID S FY N V NRSRMNVP Sbjct: 242 TFAIYVAGLVFKWLKQLGGLERMAEINARKARLLYDAIDESRGFYANPVETRNRSRMNVP 301 Query: 302 FQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRH 361 F LAD+A+D+ FL+ + + GL LKGHR VGGMRASIYNAMP GV+ L D++ +F R+H Sbjct: 302 FTLADAAMDEAFLKGARSHGLIQLKGHRSVGGMRASIYNAMPEAGVQILADYLRDFARQH 361 Query: 362 G 362 G Sbjct: 362 G 362 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: 414 Number of extensions: 15 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: 362 Length of database: 362 Length adjustment: 29 Effective length of query: 333 Effective length of database: 333 Effective search space: 110889 Effective search space used: 110889 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_012536419.1 AFE_RS04200 (3-phosphoserine/phosphohydroxythreonine aminotransferase)
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.3748.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-160 519.4 0.0 2.4e-160 519.2 0.0 1.0 1 lcl|NCBI__GCF_000021485.1:WP_012536419.1 AFE_RS04200 3-phosphoserine/phos Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021485.1:WP_012536419.1 AFE_RS04200 3-phosphoserine/phosphohydroxythreonine aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 519.2 0.0 2.4e-160 2.4e-160 1 358 [] 5 361 .. 5 361 .. 0.99 Alignments for each domain: == domain 1 score: 519.2 bits; conditional E-value: 2.4e-160 TIGR01364 1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlfl 69 i+nFsaGPa+lp+ vle++q+elld++g+g+svme+sHR ef+k++ eae+dlr+Ll+ip ny++lfl lcl|NCBI__GCF_000021485.1:WP_012536419.1 5 IFNFSAGPAVLPHVVLEQVQAELLDWHGSGMSVMEMSHRGPEFMKIAAEAEQDLRDLLDIPANYKILFL 73 68******************************************************************* PP TIGR01364 70 qGGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelke 138 qGGat qfa+vplnl++ + +a+y++tG wskka++ea+++t v+++as+e+++ s +p + ++++++ lcl|NCBI__GCF_000021485.1:WP_012536419.1 74 QGGATLQFAMVPLNLMRGHGKASYVQTGIWSKKAIAEARRFTA-VEIAASNEDRHASYVPMQADWQVSP 141 *****************************************98.************************* PP TIGR01364 139 daayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivr 207 d+ayv+++ neti Gvef+ +p+ ++plv+D ss+ils++ dvs++gliyaGaqKniGpaG+t+vivr lcl|NCBI__GCF_000021485.1:WP_012536419.1 142 DTAYVHITGNETIGGVEFDFIPDLGDIPLVSDASSHILSKPTDVSRFGLIYAGAQKNIGPAGLTLVIVR 210 ********************************************************************* PP TIGR01364 208 kdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeai 276 +dll++a ++++++ldY++ a+++s++ntpptfaiyv+glv+kwlk+ GG++++++ n +Ka+llY+ai lcl|NCBI__GCF_000021485.1:WP_012536419.1 211 DDLLGHAPANTATMLDYAVYAKEESMHNTPPTFAIYVAGLVFKWLKQLGGLERMAEINARKARLLYDAI 279 ********************************************************************* PP TIGR01364 277 desegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevq 345 des gfy n+ve ++Rs+mnv+Ftl+++ +++ Flk a+++gl++lkGhrsvGG+RasiYna+p ++vq lcl|NCBI__GCF_000021485.1:WP_012536419.1 280 DESRGFYANPVETRNRSRMNVPFTLADAAMDEAFLKGARSHGLIQLKGHRSVGGMRASIYNAMPEAGVQ 348 ********************************************************************* PP TIGR01364 346 aLvdfmkeFekkh 358 L+d++++F+++h lcl|NCBI__GCF_000021485.1:WP_012536419.1 349 ILADYLRDFARQH 361 *********9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (358 nodes) Target sequences: 1 (362 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.64 // [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