Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate PP_1768 PP_1768 phosphoserine aminotransferase
Query= BRENDA::P23721 (362 letters) >FitnessBrowser__Putida:PP_1768 Length = 361 Score = 413 bits (1062), Expect = e-120 Identities = 206/358 (57%), Positives = 259/358 (72%), Gaps = 2/358 (0%) Query: 5 FNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNVP 64 FNF +GPA LP VL++AQ E+ DW G G SVME+SHR +++ +AE+AE+D RDLL+VP Sbjct: 6 FNFCAGPAALPDAVLQRAQAEMLDWRGKGLSVMEMSHRSDDYVAIAEKAEQDLRDLLSVP 65 Query: 65 SNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKVT 124 SNYKVLF GG QFA +PLN+L + TADY++ G W+ AI+EA+++ NV Sbjct: 66 SNYKVLFLQGGASQQFAEIPLNLLPENGTADYIETGIWSKKAIEEARRFGNVNVAATAKP 125 Query: 125 VDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSRPI 184 D L A+ EW L+ NAAY+HY NETI G+ D P G DV + D SS ILSRPI Sbjct: 126 YDYL-AIPGQNEWNLTKNAAYVHYASNETIGGLQFDWVPQTG-DVPLVVDMSSDILSRPI 183 Query: 185 DVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPTF 244 DVS++G+IYAGAQKNIGP+GL +VIVREDLLG A +CP++LDY + DNGSM+NTP T+ Sbjct: 184 DVSQFGLIYAGAQKNIGPSGLVVVIVREDLLGHARSSCPTMLDYKVSADNGSMYNTPATY 243 Query: 245 AWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVPFQL 304 +WYLSGLVF+WLK GGV M++ N+ K + LYG ID S+FY N ++ RS MNVPF+L Sbjct: 244 SWYLSGLVFEWLKEQGGVEAMEQRNRAKKDRLYGFIDRSEFYTNPISVNARSWMNVPFRL 303 Query: 305 ADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRHG 362 AD LDK FL + A GL LKGHR VGGMRASIYNA+ LE V+AL +M EFE+ HG Sbjct: 304 ADERLDKAFLAGADARGLLNLKGHRSVGGMRASIYNALGLEAVEALVGYMAEFEKEHG 361 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: 410 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: 361 Length adjustment: 29 Effective length of query: 333 Effective length of database: 332 Effective search space: 110556 Effective search space used: 110556 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 PP_1768 PP_1768 (phosphoserine 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.12141.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-166 539.2 0.0 2.3e-166 539.0 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_1768 PP_1768 phosphoserine aminotrans Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_1768 PP_1768 phosphoserine aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 539.0 0.0 2.3e-166 2.3e-166 2 358 .] 6 360 .. 5 360 .. 0.99 Alignments for each domain: == domain 1 score: 539.0 bits; conditional E-value: 2.3e-166 TIGR01364 2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGattq 76 +nF+aGPaalp++vl++aq+e+ld++g+glsvme+sHRs+++ +++e+ae+dlr+Ll++p+ny+vlflqGGa++q lcl|FitnessBrowser__Putida:PP_1768 6 FNFCAGPAALPDAVLQRAQAEMLDWRGKGLSVMEMSHRSDDYVAIAEKAEQDLRDLLSVPSNYKVLFLQGGASQQ 80 8************************************************************************** PP TIGR01364 77 faavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelkedaayvylcaneti 151 fa++plnll e+ +adyi tG wskka++ea+++++ v+v+a+++ +y +ip ++e++l+++aayv++++neti lcl|FitnessBrowser__Putida:PP_1768 81 FAEIPLNLLPENGTADYIETGIWSKKAIEEARRFGN-VNVAATAKPYDYLAIPGQNEWNLTKNAAYVHYASNETI 154 **********************************99.************************************** PP TIGR01364 152 eGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelpsvldYki 226 G++f+++p++ ++plv+D+ssdilsr+idvs++gliyaGaqKniGp+G++vvivr+dll++a++++p++ldYk+ lcl|FitnessBrowser__Putida:PP_1768 155 GGLQFDWVPQTGDVPLVVDMSSDILSRPIDVSQFGLIYAGAQKNIGPSGLVVVIVREDLLGHARSSCPTMLDYKV 229 *************************************************************************** PP TIGR01364 227 laendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaRslmnvvFtl 301 a+n s+yntp+t+++y++glv++wlke+GGv+++e++n++K++ lY id+se fy+n+++ +aRs+mnv+F+l lcl|FitnessBrowser__Putida:PP_1768 230 SADNGSMYNTPATYSWYLSGLVFEWLKEQGGVEAMEQRNRAKKDRLYGFIDRSE-FYTNPISVNARSWMNVPFRL 303 ***************************************************996.******************** PP TIGR01364 302 kkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekkh 358 ++e+l+k Fl+ a ++gl++lkGhrsvGG+RasiYnal le+v+aLv +m eFek+h lcl|FitnessBrowser__Putida:PP_1768 304 ADERLDKAFLAGADARGLLNLKGHRSVGGMRASIYNALGLEAVEALVGYMAEFEKEH 360 ******************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (358 nodes) Target sequences: 1 (361 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: 7.30 // [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