Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_028488900.1 Q394_RS0108430 3-phosphoserine/phosphohydroxythreonine transaminase
Query= BRENDA::Q96255 (430 letters) >NCBI__GCF_000621325.1:WP_028488900.1 Length = 361 Score = 407 bits (1046), Expect = e-118 Identities = 202/359 (56%), Positives = 259/359 (72%) Query: 71 ERVFNFAAGPATLPENVLLKAQADLYNWRGSGMSVMEMSHRGKEFLSIIQKAESDLRQLL 130 +R+FNF+AGPA LP++VL +AQA++ +W GSGMSVMEMSHRG E++SI +AE+DLR+++ Sbjct: 2 KRIFNFSAGPAMLPQSVLEQAQAEMLDWNGSGMSVMEMSHRGHEYMSIAAEAEADLREIM 61 Query: 131 EIPQEYSVLFLQGGATTQFAALPLNLCKSDDTVDFVVTGSWGDKAVKEAKKYCKTNVIWS 190 IP Y VLFLQGGA++QFA +P NL + T D+V TG W DKA+ EAK+Y K NV+ S Sbjct: 62 GIPSNYKVLFLQGGASSQFAMIPQNLLRGKGTADYVDTGDWSDKAIMEAKRYGKVNVVAS 121 Query: 191 GKSEKYTKVPSFEELEQTPDAKYLHICANETIHGVEFKDYPVPKNGFLVADMSSNFCSKP 250 K YT VP+F+ + +A YLH NETI GVEF P + LVADMSS S+P Sbjct: 122 SKIGNYTSVPAFDTWTRDANAAYLHYTPNETIRGVEFGWIPETGDVPLVADMSSTILSRP 181 Query: 251 VDVSKFGVIYGGAQKNVGPSGVTIVIIRKDLIGNAQDITPVMLDYKIHDENSSLYNTPPC 310 +DVSKFG+IY GAQKN+GP+G+TIVI+R DLIG TP M DYKIH +N S+YNTP Sbjct: 182 LDVSKFGLIYAGAQKNIGPAGLTIVIVRDDLIGETLPGTPTMFDYKIHADNESMYNTPAT 241 Query: 311 FGIYMCGLVFEDLLEQGGLKEVEKKNQRKADLLYNAIEESNGFFRCPVEKSVRSLMNVPF 370 + Y+ GLVF+ + +QGGL + NQRKA LY AIE S GF+ PV RS MNVPF Sbjct: 242 YSWYLAGLVFKWIKQQGGLAGMATLNQRKAQKLYTAIETSGGFYHSPVAPDCRSWMNVPF 301 Query: 371 TLEKSELEAEFIKEAAKEKMVQLKGHRSVGGMRASIYNAMPLAGVEKLVAFMKDFQAKH 429 L +EL+ F+ EAA++ ++ LKGHR GGMRAS+YNAMP AGV+ LV+FM+DF K+ Sbjct: 302 ILANAELDKSFLSEAAQQGLMTLKGHRLFGGMRASLYNAMPEAGVDTLVSFMQDFAKKN 360 Lambda K H 0.316 0.132 0.381 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: 432 Number of extensions: 8 Number of successful extensions: 1 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: 430 Length of database: 361 Length adjustment: 31 Effective length of query: 399 Effective length of database: 330 Effective search space: 131670 Effective search space used: 131670 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: 50 (23.9 bits)
Align candidate WP_028488900.1 Q394_RS0108430 (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.12560.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-163 529.4 0.0 2.1e-163 529.3 0.0 1.0 1 lcl|NCBI__GCF_000621325.1:WP_028488900.1 Q394_RS0108430 3-phosphoserine/p Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000621325.1:WP_028488900.1 Q394_RS0108430 3-phosphoserine/phosphohydroxythreonine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 529.3 0.0 2.1e-163 2.1e-163 1 358 [] 4 360 .. 4 360 .. 0.99 Alignments for each domain: == domain 1 score: 529.3 bits; conditional E-value: 2.1e-163 TIGR01364 1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlfl 69 i+nFsaGPa+lp++vle+aq+e+ld+ng+g+svme+sHR +e+++++ eae dlre++ ip+ny+vlfl lcl|NCBI__GCF_000621325.1:WP_028488900.1 4 IFNFSAGPAMLPQSVLEQAQAEMLDWNGSGMSVMEMSHRGHEYMSIAAEAEADLREIMGIPSNYKVLFL 72 68******************************************************************* PP TIGR01364 70 qGGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelke 138 qGGa++qfa++p nll+ k +ady+ tG ws+ka+ eak+++k v+vvas++ ++y+++p ++++ + lcl|NCBI__GCF_000621325.1:WP_028488900.1 73 QGGASSQFAMIPQNLLRGKGTADYVDTGDWSDKAIMEAKRYGK-VNVVASSKIGNYTSVPAFDTWTRDA 140 *****************************************99.************************* PP TIGR01364 139 daayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivr 207 +aay++++ neti+Gvef ++pe+ ++plvaD+ss ilsr++dvsk+gliyaGaqKniGpaG+t+vivr lcl|NCBI__GCF_000621325.1:WP_028488900.1 141 NAAYLHYTPNETIRGVEFGWIPETGDVPLVADMSSTILSRPLDVSKFGLIYAGAQKNIGPAGLTIVIVR 209 ********************************************************************* PP TIGR01364 208 kdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeai 276 +dl++++ +p+++dYki+a+n+s+yntp+t+++y++glv+kw+k++GG++ ++ nq+Ka+ lY ai lcl|NCBI__GCF_000621325.1:WP_028488900.1 210 DDLIGETLPGTPTMFDYKIHADNESMYNTPATYSWYLAGLVFKWIKQQGGLAGMATLNQRKAQKLYTAI 278 ********************************************************************* PP TIGR01364 277 desegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevq 345 ++s gfy+++v++++Rs+mnv+F l+++el+k+Fl+ea+++gl++lkGhr GG+Ras+Yna+p ++v lcl|NCBI__GCF_000621325.1:WP_028488900.1 279 ETSGGFYHSPVAPDCRSWMNVPFILANAELDKSFLSEAAQQGLMTLKGHRLFGGMRASLYNAMPEAGVD 347 ********************************************************************* PP TIGR01364 346 aLvdfmkeFekkh 358 +Lv+fm++F+kk+ lcl|NCBI__GCF_000621325.1:WP_028488900.1 348 TLVSFMQDFAKKN 360 **********985 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.73 // [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