Align Phosphoserine phosphatase; PSP; PSPase; EC 3.1.3.3 (characterized)
to candidate WP_035241316.1 Q366_RS17130 bifunctional phosphoserine phosphatase/homoserine phosphotransferase ThrH
Query= SwissProt::Q883R9 (237 letters) >NCBI__GCF_000745975.1:WP_035241316.1 Length = 201 Score = 219 bits (559), Expect = 2e-62 Identities = 106/192 (55%), Positives = 137/192 (71%) Query: 33 VEIACLDLEGVLVPEIWIAFAEKTGIESLRATTRDIPDYDVLMKQRLRILDEHGLKLADI 92 ++I DLEGV +PEIWI A+KTGIE L+ TTRDI DYDVLM +RL ILDEH L L DI Sbjct: 1 MKILVADLEGVFLPEIWINVAKKTGIEELKLTTRDISDYDVLMTKRLSILDEHHLTLKDI 60 Query: 93 QAVISTLKPLEGAVEFVDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHRLITDETD 152 Q VI+ L+PL+GA + +DW+R++ Q++ILSDTF EF+ PLM +LGFP LLCH L D T+ Sbjct: 61 QGVIAGLEPLDGAKQMLDWIRKQTQIIILSDTFEEFAGPLMEKLGFPALLCHNLTVDATN 120 Query: 153 RVVSYQLRQKDPKRQSVLAFKSLYYRIIAAGDSYNDTTMLGEADAGILFHAPDNVIREFP 212 R+ Y LR + K ++V A + L Y +IA GDSYNDT M+ AD G F PD++ +FP Sbjct: 121 RITGYNLRIDNQKARAVNALQGLNYHVIAFGDSYNDTGMILAADQGFFFKPPDSITEDFP 180 Query: 213 QFPAVHTFDELK 224 P ++DELK Sbjct: 181 DIPITRSYDELK 192 Lambda K H 0.324 0.139 0.410 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: 155 Number of extensions: 5 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: 237 Length of database: 201 Length adjustment: 22 Effective length of query: 215 Effective length of database: 179 Effective search space: 38485 Effective search space used: 38485 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 45 (21.9 bits)
Align candidate WP_035241316.1 Q366_RS17130 (bifunctional phosphoserine phosphatase/homoserine phosphotransferase ThrH)
to HMM TIGR02137 (thrH: phosphoserine phosphatase/homoserine phosphotransferase bifunctional protein (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/TIGR02137.hmm # target sequence database: /tmp/gapView.27835.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02137 [M=203] Accession: TIGR02137 Description: HSK-PSP: phosphoserine phosphatase/homoserine phosphotransferase bifunctional protein 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-87 278.6 0.1 1.5e-87 278.4 0.1 1.0 1 lcl|NCBI__GCF_000745975.1:WP_035241316.1 Q366_RS17130 bifunctional phosph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745975.1:WP_035241316.1 Q366_RS17130 bifunctional phosphoserine phosphatase/homoserine phosphotrans # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 278.4 0.1 1.5e-87 1.5e-87 1 193 [. 1 193 [. 1 199 [. 0.98 Alignments for each domain: == domain 1 score: 278.4 bits; conditional E-value: 1.5e-87 TIGR02137 1 qevvtldlegvlvpeiwiavaektgiddlklttrdipdydvlmkqrlkileeenlklsdiqeviatlkl 69 +++ + dlegv+ peiwi va+ktgi++lklttrdi dydvlm +rl il+e+ l l diq via l++ lcl|NCBI__GCF_000745975.1:WP_035241316.1 1 MKILVADLEGVFLPEIWINVAKKTGIEELKLTTRDISDYDVLMTKRLSILDEHHLTLKDIQGVIAGLEP 69 578899*************************************************************** PP TIGR02137 70 legavefvdtlreeaqvvilsdtfqefaqplmkqlgfptllchklvvedsdrvkgyqlrqkdqkrkvvk 138 l+ga++++d++r++ q++ilsdtf efa plm +lgfp+llch+l v+ ++r+ gy+lr ++qk ++v lcl|NCBI__GCF_000745975.1:WP_035241316.1 70 LDGAKQMLDWIRKQTQIIILSDTFEEFAGPLMEKLGFPALLCHNLTVDATNRITGYNLRIDNQKARAVN 138 ********************************************************************* PP TIGR02137 139 alkelyykviaagdsyndttmlkeadkgilfhapesvvaefpqleavktyeelkd 193 al+ l+y+via gdsyndt+m+ ad+g +f+ p+s+ +fp+++ +++y+elk lcl|NCBI__GCF_000745975.1:WP_035241316.1 139 ALQGLNYHVIAFGDSYNDTGMILAADQGFFFKPPDSITEDFPDIPITRSYDELKV 193 *****************************************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (203 nodes) Target sequences: 1 (201 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 6.04 // [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