Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate PfGW456L13_2175 Phosphoserine aminotransferase (EC 2.6.1.52)
Query= BRENDA::P23721 (362 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2175 Length = 363 Score = 409 bits (1051), Expect = e-119 Identities = 204/358 (56%), Positives = 254/358 (70%), Gaps = 2/358 (0%) Query: 5 FNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNVP 64 +NF +GPA LP VL++AQ EL DW+G G SVME+SHR EF+ +A +AE+D RDLLN+P Sbjct: 8 YNFCAGPAALPEAVLQRAQGELLDWHGKGLSVMEMSHRSDEFVSIATKAEQDLRDLLNIP 67 Query: 65 SNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKVT 124 SNYKVLF GG QFA +PLN+L + +ADY+D G W+ AI+EA ++ NV Sbjct: 68 SNYKVLFLQGGASQQFAQIPLNLLPENGSADYIDTGIWSQKAIEEASRFGHVNVAATAKP 127 Query: 125 VDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSRPI 184 D A+ EW+LS +AAY+HY PNETI G+ P+ G DV + AD SS ILSRP+ Sbjct: 128 YDYF-AIPGQNEWKLSKDAAYVHYAPNETIGGLEFQWIPETG-DVPLVADMSSDILSRPV 185 Query: 185 DVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPTF 244 DVSR+G+IYAGAQKNIGP+G+ + IVREDLLGKA CP++LDY + DNGSM+NTPPT Sbjct: 186 DVSRFGMIYAGAQKNIGPSGIVVNIVREDLLGKARSLCPTMLDYKVAADNGSMYNTPPTL 245 Query: 245 AWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVPFQL 304 AWYLSGLVF+WLK GGV + K+N+ K LY ID S Y N + K++RS MNVPF+L Sbjct: 246 AWYLSGLVFEWLKEQGGVEAIGKLNEVKQRTLYSFIDASGLYSNPINKSDRSWMNVPFRL 305 Query: 305 ADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRHG 362 AD LDK FL + GL LKGHR VGGMRASIYNA+ + V AL +M EFE+ HG Sbjct: 306 ADDRLDKPFLAGADERGLLNLKGHRSVGGMRASIYNAVDINAVNALISYMAEFEKEHG 363 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: 418 Number of extensions: 13 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: 363 Length adjustment: 29 Effective length of query: 333 Effective length of database: 334 Effective search space: 111222 Effective search space used: 111222 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 PfGW456L13_2175 (Phosphoserine aminotransferase (EC 2.6.1.52))
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.26091.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-164 532.0 0.0 3.6e-164 531.8 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2175 Phosphoserine aminotransferase ( Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2175 Phosphoserine aminotransferase (EC 2.6.1.52) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 531.8 0.0 3.6e-164 3.6e-164 2 358 .] 8 362 .. 7 362 .. 0.99 Alignments for each domain: == domain 1 score: 531.8 bits; conditional E-value: 3.6e-164 TIGR01364 2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlre 56 +nF+aGPaalpe+vl++aq elld++g+glsvme+sHRs+ef +++++ae+dlr+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2175 8 YNFCAGPAALPEAVLQRAQGELLDWHGKGLSVMEMSHRSDEFVSIATKAEQDLRD 62 8****************************************************** PP TIGR01364 57 LlnipdnyevlflqGGattqfaavplnllkekkvadyivtGawskkalkeakklt 111 Llnip+ny+vlflqGGa++qfa++plnll e+ adyi tG ws+ka++ea++++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2175 63 LLNIPSNYKVLFLQGGASQQFAQIPLNLLPENGSADYIDTGIWSQKAIEEASRFG 117 ******************************************************9 PP TIGR01364 112 kevkvvaseeekkyskipdeeelelkedaayvylcanetieGvefkelpevkkap 166 + v+v+a+++ +y +ip ++e++l++daayv+++ neti G+ef+++pe+ ++p lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2175 118 H-VNVAATAKPYDYFAIPGQNEWKLSKDAAYVHYAPNETIGGLEFQWIPETGDVP 171 9.***************************************************** PP TIGR01364 167 lvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelpsv 221 lvaD+ssdilsr++dvs++g+iyaGaqKniGp+G++v ivr+dll++a++ +p++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2175 172 LVADMSSDILSRPVDVSRFGMIYAGAQKNIGPSGIVVNIVREDLLGKARSLCPTM 226 ******************************************************* PP TIGR01364 222 ldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeai 276 ldYk++a+n s+yntppt a+y++glv++wlke+GGv+++ k n+ K + lY i lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2175 227 LDYKVAADNGSMYNTPPTLAWYLSGLVFEWLKEQGGVEAIGKLNEVKQRTLYSFI 281 ******************************************************* PP TIGR01364 277 desegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGi 331 d+s g+y n+++k++Rs+mnv+F+l++++l+k Fl+ a e+gl++lkGhrsvGG+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2175 282 DAS-GLYSNPINKSDRSWMNVPFRLADDRLDKPFLAGADERGLLNLKGHRSVGGM 335 *99.6************************************************** PP TIGR01364 332 RasiYnalpleevqaLvdfmkeFekkh 358 RasiYna+ +++v+aL+++m eFek+h lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2175 336 RASIYNAVDINAVNALISYMAEFEKEH 362 ************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (358 nodes) Target sequences: 1 (363 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: 8.74 // [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