Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate N515DRAFT_1430 N515DRAFT_1430 phosphoserine aminotransferase apoenzyme
Query= BRENDA::Q96255 (430 letters) >FitnessBrowser__Dyella79:N515DRAFT_1430 Length = 361 Score = 380 bits (976), Expect = e-110 Identities = 184/358 (51%), Positives = 254/358 (70%) Query: 72 RVFNFAAGPATLPENVLLKAQADLYNWRGSGMSVMEMSHRGKEFLSIIQKAESDLRQLLE 131 RV+NF+AGPA +P VL +AQ +L +W GSG SVME+SHRGK F+ + ++AE+DLR+LL+ Sbjct: 3 RVWNFSAGPAAIPTAVLERAQRELLDWNGSGASVMELSHRGKRFIGLAEQAEADLRELLK 62 Query: 132 IPQEYSVLFLQGGATTQFAALPLNLCKSDDTVDFVVTGSWGDKAVKEAKKYCKTNVIWSG 191 IP +Y+VLFLQGGAT FA +PLNL D+ D++V G WG+KA EA Y + NV S Sbjct: 63 IPADYAVLFLQGGATQHFAQIPLNLAGEGDSADYIVNGHWGEKAASEAASYVRVNVAASS 122 Query: 192 KSEKYTKVPSFEELEQTPDAKYLHICANETIHGVEFKDYPVPKNGFLVADMSSNFCSKPV 251 ++E+Y ++P + P A Y+H NETIHGVE+ D P LVADMSSN ++P+ Sbjct: 123 RNEQYLRLPPRASWQLDPRAAYVHYTPNETIHGVEYHDVPEVGEVPLVADMSSNILAEPL 182 Query: 252 DVSKFGVIYGGAQKNVGPSGVTIVIIRKDLIGNAQDITPVMLDYKIHDENSSLYNTPPCF 311 DVS+FG+IY GAQKN+GPSG+ ++IIR+DL+ A + Y H N S+ NTP + Sbjct: 183 DVSRFGLIYAGAQKNIGPSGLVVMIIRRDLLQRAARPMAKIFRYAEHAANDSMLNTPNTW 242 Query: 312 GIYMCGLVFEDLLEQGGLKEVEKKNQRKADLLYNAIEESNGFFRCPVEKSVRSLMNVPFT 371 G Y+ GL F+ L EQGGL+ + +N+ KA LLY AI+ S G++R P++ + RS MNVPFT Sbjct: 243 GWYLAGLTFQWLKEQGGLEAMAHRNRDKAGLLYQAIDGSGGYYRNPIDPAARSRMNVPFT 302 Query: 372 LEKSELEAEFIKEAAKEKMVQLKGHRSVGGMRASIYNAMPLAGVEKLVAFMKDFQAKH 429 L S L+A+F+KE+ ++ LKGH+++GGMRAS+YNA+PL V+ LV FM+DF A+H Sbjct: 303 LHDSALDADFLKESEAAGLLALKGHKALGGMRASLYNAVPLEAVQVLVQFMRDFAARH 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: 362 Number of extensions: 10 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 N515DRAFT_1430 N515DRAFT_1430 (phosphoserine aminotransferase apoenzyme)
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.20649.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-159 515.5 0.0 3.7e-159 515.3 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_1430 N515DRAFT_1430 phosphoserine ami Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_1430 N515DRAFT_1430 phosphoserine aminotransferase apoenzyme # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 515.3 0.0 3.7e-159 3.7e-159 2 358 .] 5 360 .. 4 360 .. 0.99 Alignments for each domain: == domain 1 score: 515.3 bits; conditional E-value: 3.7e-159 TIGR01364 2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevl 67 nFsaGPaa+p++vle+aq+elld+ng+g+svme+sHR k+f ++e+ae dlreLl+ip +y+vl lcl|FitnessBrowser__Dyella79:N515DRAFT_1430 5 WNFSAGPAAIPTAVLERAQRELLDWNGSGASVMELSHRGKRFIGLAEQAEADLRELLKIPADYAVL 70 7***************************************************************** PP TIGR01364 68 flqGGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeee 133 flqGGat+ fa++plnl+ e++ adyiv G+w++ka++ea +++ v+v+as+++++y ++p + + lcl|FitnessBrowser__Dyella79:N515DRAFT_1430 71 FLQGGATQHFAQIPLNLAGEGDSADYIVNGHWGEKAASEAASYVR-VNVAASSRNEQYLRLPPRAS 135 *******************************************99.******************** PP TIGR01364 134 lelkedaayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpa 199 ++l+++aayv+++ neti+Gve++++pev ++plvaD+ss+il++++dvs++gliyaGaqKniGp+ lcl|FitnessBrowser__Dyella79:N515DRAFT_1430 136 WQLDPRAAYVHYTPNETIHGVEYHDVPEVGEVPLVADMSSNILAEPLDVSRFGLIYAGAQKNIGPS 201 ****************************************************************** PP TIGR01364 200 GvtvvivrkdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekkn 265 G++v+i+r+dll+ra + ++++++Y+ +a nds++ntp t+++y++gl+++wlke+GG+++++++n lcl|FitnessBrowser__Dyella79:N515DRAFT_1430 202 GLVVMIIRRDLLQRAARPMAKIFRYAEHAANDSMLNTPNTWGWYLAGLTFQWLKEQGGLEAMAHRN 267 ****************************************************************** PP TIGR01364 266 qeKakllYeaidesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGi 331 ++Ka llY+aid s g+y+n+++++aRs+mnv+Ftl+++ l++ Flke+e++gl++lkGh+++GG+ lcl|FitnessBrowser__Dyella79:N515DRAFT_1430 268 RDKAGLLYQAIDGSGGYYRNPIDPAARSRMNVPFTLHDSALDADFLKESEAAGLLALKGHKALGGM 333 ****************************************************************** PP TIGR01364 332 RasiYnalpleevqaLvdfmkeFekkh 358 Ras+Yna+ple+vq Lv+fm++F+++h lcl|FitnessBrowser__Dyella79:N515DRAFT_1430 334 RASLYNAVPLEAVQVLVQFMRDFAARH 360 ***********************9987 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.22 // [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