Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate 350681 BT1153 phosphoserine aminotransferase (NCBI ptt file)
Query= SwissProt::Q59196 (362 letters) >FitnessBrowser__Btheta:350681 Length = 355 Score = 301 bits (772), Expect = 1e-86 Identities = 160/359 (44%), Positives = 236/359 (65%), Gaps = 10/359 (2%) Query: 4 RAYNFNAGPAALPLEVLERAQAEFVDYQHTGMSIMEMSHRGAVYEAVHNEAQARLLALLG 63 + +NFNAGP+ LP EV+E +D+ +G+S+ME+SHR ++ V +EA+A LL Sbjct: 2 KKHNFNAGPSILPREVIEDTAKAILDFNGSGLSLMEISHRAKDFQPVVDEAEALFKELLN 61 Query: 64 NPTGYKVLFIQGGASTQFAMIPMNFLKEGQTANYVMTGSWASKALKEAKLIGDTHVAASS 123 P GY VLF+ GGAS +F M+P NFL++ A Y+ TG WA KA+KEAK G+ ASS Sbjct: 62 IPEGYSVLFLGGGASMEFCMVPFNFLEK--KAAYLNTGVWAKKAMKEAKGFGEVVEVASS 119 Query: 124 EASNYMTLPKLQEIQLQDNAAYLHLTSNETIEGAQFKAFPDTGS-VPLIGDMSSDILSRP 182 + Y +PK + + +A Y H+T+N TI G + K D S VP++ DMSSDI SRP Sbjct: 120 AEATYTYIPK--DYTIPADADYFHITTNNTIYGTELKE--DLNSPVPMVADMSSDIFSRP 175 Query: 183 FDLNQFGLVYAGAQKNLGPSGVTVVIVREDLVAESPKHLPTMLRYDTYVKNNSLYNTPPS 242 D++++ +Y GAQKNL P+GVT VIV+ D V + +++P+ML Y T++ N S++NTPP Sbjct: 176 IDVSKYICIYGGAQKNLAPAGVTFVIVKNDAVGKVSRYIPSMLNYQTHIDNGSMFNTPPV 235 Query: 243 FGIYMVNEVLKWIEERGGLEGVQQANRKKASLIYDAIDQSGGFYRGCVDVDSRSDMNITF 302 IY L+WI+ +GG++ +++ +KA ++Y ID++ F G + RS MNI F Sbjct: 236 VPIYAALLNLRWIKAQGGVKEMERRAIEKADMLYAEIDRNKLFV-GTAAKEDRSRMNICF 294 Query: 303 RLASE--ELEKEFVKASEQEGFVGLKGHRSVGGLRASIYNAVPYESCEALVQFMEHFKR 359 +A E +LE +F+K + ++G VG+KGHRSVGG RAS YNA+P ES +AL+ M+ F++ Sbjct: 295 VMAPEYKDLEADFMKFATEKGMVGIKGHRSVGGFRASCYNALPKESVQALIDCMQEFEK 353 Lambda K H 0.316 0.132 0.378 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: 335 Number of extensions: 21 Number of successful extensions: 5 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: 355 Length adjustment: 29 Effective length of query: 333 Effective length of database: 326 Effective search space: 108558 Effective search space used: 108558 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: 49 (23.5 bits)
Align candidate 350681 BT1153 (phosphoserine aminotransferase (NCBI ptt file))
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.13824.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-139 449.4 0.0 4.6e-139 449.2 0.0 1.0 1 lcl|FitnessBrowser__Btheta:350681 BT1153 phosphoserine aminotransf Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:350681 BT1153 phosphoserine aminotransferase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 449.2 0.0 4.6e-139 4.6e-139 2 358 .] 4 355 .] 3 355 .] 0.97 Alignments for each domain: == domain 1 score: 449.2 bits; conditional E-value: 4.6e-139 TIGR01364 2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGattqf 77 +nF+aGP++lp+ev+e+ +k +ldfng+gls+meisHR+k+f+ vv+eae ++eLlnip+ y+vlfl GGa+ +f lcl|FitnessBrowser__Btheta:350681 4 HNFNAGPSILPREVIEDTAKAILDFNGSGLSLMEISHRAKDFQPVVDEAEALFKELLNIPEGYSVLFLGGGASMEF 79 8*************************************************************************** PP TIGR01364 78 aavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelkedaayvylcanetieG 153 +vp+n+l++k a+y++tG+w+kka+keak +++ v vas++e y+ ip +++++ da+y+++++n+ti+G lcl|FitnessBrowser__Btheta:350681 80 CMVPFNFLEKK--AAYLNTGVWAKKAMKEAKGFGE-VVEVASSAEATYTYIP--KDYTIPADADYFHITTNNTIYG 150 ********988..********************99.66677777899*****..8899999*************** PP TIGR01364 154 vefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelpsvldYkilae 229 +e ke ++ +p+vaD+ssdi+sr+idvsky iy+GaqKn+ paGvt+viv++d +++ ++ +ps+l+Y+++++ lcl|FitnessBrowser__Btheta:350681 151 TELKEDL-NSPVPMVADMSSDIFSRPIDVSKYICIYGGAQKNLAPAGVTFVIVKNDAVGKVSRYIPSMLNYQTHID 225 ****999.789***************************************************************** PP TIGR01364 230 ndslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaRslmnvvFtlkke. 304 n s++ntpp++ iy++ l l+w+k++GGvk++e++ eKa++lY id++ +++ ++++k++Rs+mn++F ++ e lcl|FitnessBrowser__Btheta:350681 226 NGSMFNTPPVVPIYAALLNLRWIKAQGGVKEMERRAIEKADMLYAEIDRN-KLFVGTAAKEDRSRMNICFVMAPEy 300 ************************************************87.6********************9988 PP TIGR01364 305 .elekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekkh 358 +le+ F+k a+ekg+v++kGhrsvGG+Ras Ynalp e+vqaL+d m+eFek h lcl|FitnessBrowser__Btheta:350681 301 kDLEADFMKFATEKGMVGIKGHRSVGGFRASCYNALPKESVQALIDCMQEFEKLH 355 8***************************************************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (358 nodes) Target sequences: 1 (355 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: 6.96 // [ok]
This GapMind analysis is from Apr 09 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