Align phosphoserine phosphatase (EC 3.1.3.3) (characterized)
to candidate WP_011779312.1 MVAN_RS10445 phosphoserine phosphatase SerB
Query= BRENDA::O53289 (409 letters) >NCBI__GCF_000015305.1:WP_011779312.1 Length = 419 Score = 620 bits (1599), Expect = 0.0 Identities = 321/402 (79%), Positives = 355/402 (88%) Query: 6 SVLITVTGMDQPGVTSALFEVLAQHGVELLNVEQVVIRGRLTLGVLVSCPLDVADGTALR 65 S+LITVTG DQPGVTSALFEVL++H V+LLNVEQVVIRGRLTLGVLV+ +VA G LR Sbjct: 17 SLLITVTGRDQPGVTSALFEVLSRHRVDLLNVEQVVIRGRLTLGVLVAAATEVAAGAELR 76 Query: 66 DDVAAAIHGVGLDVAIERSDDLPIIRQPSTHTIFVLGRPITAGAFSAVARGVAALGVNID 125 +V AAIHGVGLDV+IE SD LP++R PSTHTI VLGRPITA AF VAR AALGVNID Sbjct: 77 SEVEAAIHGVGLDVSIESSDGLPVLRVPSTHTIVVLGRPITAEAFGVVAREAAALGVNID 136 Query: 126 FIRGISDYPVTGLELRVSVPPGCVGPLQIALTKVAAEEHVDVAVEDYGLAWRTKRLIVFD 185 FIRG+SDYPVTGLELRVSVPPG LQ L +VA EE VD+AVEDY L+ R KRLIVFD Sbjct: 137 FIRGVSDYPVTGLELRVSVPPGAYRELQAVLARVAVEESVDIAVEDYSLSRRAKRLIVFD 196 Query: 186 VDSTLVQGEVIEMLAARAGAQGQVAAITEAAMRGELDFAESLQRRVATLAGLPATVIDDV 245 VDSTL+QGEVIEMLAA AGA+ VA +TEAAMRGELDFAESL RRVATLAGLPA+V+DDV Sbjct: 197 VDSTLIQGEVIEMLAAHAGAEAAVAEVTEAAMRGELDFAESLHRRVATLAGLPASVLDDV 256 Query: 246 AEQLELMPGARTTIRTLRRLGFRCGVVSGGFRRIIEPLARELMLDFVASNELEIVDGILT 305 A+Q+EL PGARTT+RTLRRLG+ CG+VSGGFR++IEPLA ELM+DFVA+NELEIVDG LT Sbjct: 257 ADQIELTPGARTTLRTLRRLGYHCGIVSGGFRQVIEPLAHELMMDFVAANELEIVDGKLT 316 Query: 306 GRVVGPIVDRPGKAKALRDFASQYGVPMEQTVAVGDGANDIDMLGAAGLGIAFNAKPALR 365 GRVVG +VDRPGKAKALRDFA Q GVPMEQTVAVGDGANDIDML AAGLG+AFNAKPALR Sbjct: 317 GRVVGDVVDRPGKAKALRDFAQQAGVPMEQTVAVGDGANDIDMLSAAGLGVAFNAKPALR 376 Query: 366 EVADASLSHPYLDTVLFLLGVTRGEIEAADAGDCGVRRVEIP 407 EVADASLS+PYLDT+LF+LG+TRGEIEAADA D VRRVEIP Sbjct: 377 EVADASLSYPYLDTLLFILGITRGEIEAADALDGVVRRVEIP 418 Lambda K H 0.321 0.139 0.395 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: 648 Number of extensions: 22 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: 409 Length of database: 419 Length adjustment: 31 Effective length of query: 378 Effective length of database: 388 Effective search space: 146664 Effective search space used: 146664 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 (21.9 bits) S2: 50 (23.9 bits)
Align candidate WP_011779312.1 MVAN_RS10445 (phosphoserine phosphatase SerB)
to HMM TIGR00338 (serB: phosphoserine phosphatase SerB (EC 3.1.3.3))
# 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/TIGR00338.hmm # target sequence database: /tmp/gapView.18218.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00338 [M=219] Accession: TIGR00338 Description: serB: phosphoserine phosphatase SerB 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-77 246.4 0.0 1.6e-77 246.0 0.0 1.1 1 lcl|NCBI__GCF_000015305.1:WP_011779312.1 MVAN_RS10445 phosphoserine phosp Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015305.1:WP_011779312.1 MVAN_RS10445 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 246.0 0.0 1.6e-77 1.6e-77 1 219 [] 177 395 .. 177 395 .. 0.99 Alignments for each domain: == domain 1 score: 246.0 bits; conditional E-value: 1.6e-77 TIGR00338 1 diakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkll 69 dia++++s +++k+l+vfD+Dstli+ EvI+ +a+ aG e +V+e+Te AmrgeldF esl+ Rv++l lcl|NCBI__GCF_000015305.1:WP_011779312.1 177 DIAVEDYSLSRRAKRLIVFDVDSTLIQGEVIEMLAAHAGAEAAVAEVTEAAMRGELDFAESLHRRVATL 245 6889999999*********************************************************** PP TIGR00338 70 kglpvellkkveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgk 138 glp+++l+ v++++elt+G++ + ++L++ gy+ ++SGgF++v+e l+ +L +d+v+aN+Le+ dgk lcl|NCBI__GCF_000015305.1:WP_011779312.1 246 AGLPASVLDDVADQIELTPGARTTLRTLRRLGYHCGIVSGGFRQVIEPLAHELMMDFVAANELEIVDGK 314 ********************************************************************* PP TIGR00338 139 ltGkvegeivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadivi 207 ltG+v g++vd kak l +++ g+++e+tvavGDGanD+ m++aAglg+afnakp+l+e+ad+++ lcl|NCBI__GCF_000015305.1:WP_011779312.1 315 LTGRVVGDVVDRPGKAKALRDFAQQAGVPMEQTVAVGDGANDIDMLSAAGLGVAFNAKPALREVADASL 383 ********************************************************************* PP TIGR00338 208 ekkdltdilell 219 + +l +l +l lcl|NCBI__GCF_000015305.1:WP_011779312.1 384 SYPYLDTLLFIL 395 *****9998776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (419 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: 00:00:00.00 # Mc/sec: 9.34 // [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