Align Phosphoserine phosphatase ThrH; PSP; PSPase; EC 3.1.3.3 (characterized)
to candidate WP_027456929.1 K420_RS0104085 bifunctional phosphoserine phosphatase/homoserine phosphotransferase ThrH
Query= SwissProt::Q9I2Y2 (205 letters) >NCBI__GCF_000519045.1:WP_027456929.1 Length = 204 Score = 254 bits (648), Expect = 1e-72 Identities = 127/198 (64%), Positives = 149/198 (75%) Query: 1 MEIACLDLEGVLVPEIWIAFAEKTGIDALKATTRDIPDYDVLMKQRLRILDEHGLKLGDI 60 M+I CLDLEGVLVPEIWI F+++TGI L TTRD PDYD LM RL IL +H L L DI Sbjct: 1 MKIVCLDLEGVLVPEIWIEFSKRTGIPELMRTTRDEPDYDKLMTYRLDILRQHKLGLPDI 60 Query: 61 QEVIATLKPLEGAVEFVDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHKLEIDDSD 120 Q+VI + P+EGA F+D LRE +QVVILSDTFYEF+ PLMRQLG+PTL CH LE D+ Sbjct: 61 QKVIGEMGPMEGARAFLDQLREDYQVVILSDTFYEFAHPLMRQLGWPTLFCHSLEDDEQG 120 Query: 121 RVVGYQLRQKDPKRQSVIAFKSLYYRVIAAGDSYNDTTMLSEAHAGILFHAPENVIREFP 180 +V Y LR D KR++V FK L ++V+AAGDSYNDT ML EAH GILFH PENVIREFP Sbjct: 121 MLVDYHLRMPDQKREAVKRFKELNFQVVAAGDSYNDTAMLGEAHGGILFHPPENVIREFP 180 Query: 181 QFPAVHTYEDLKREFLKA 198 QFP +Y+ L+ E KA Sbjct: 181 QFPVALSYDQLRAEIDKA 198 Lambda K H 0.323 0.140 0.408 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: 185 Number of extensions: 6 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: 205 Length of database: 204 Length adjustment: 21 Effective length of query: 184 Effective length of database: 183 Effective search space: 33672 Effective search space used: 33672 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 45 (21.9 bits)
Align candidate WP_027456929.1 K420_RS0104085 (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.21561.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.6e-92 292.4 0.0 9.1e-92 292.1 0.0 1.0 1 lcl|NCBI__GCF_000519045.1:WP_027456929.1 K420_RS0104085 bifunctional phos Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000519045.1:WP_027456929.1 K420_RS0104085 bifunctional phosphoserine phosphatase/homoserine phosphotra # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 292.1 0.0 9.1e-92 9.1e-92 1 198 [. 1 198 [. 1 202 [. 0.99 Alignments for each domain: == domain 1 score: 292.1 bits; conditional E-value: 9.1e-92 TIGR02137 1 qevvtldlegvlvpeiwiavaektgiddlklttrdipdydvlmkqrlkileeenlklsdiqeviatlkl 69 +++v+ldlegvlvpeiwi ++++tgi +l ttrd pdyd lm rl il +++l l diq+vi ++++ lcl|NCBI__GCF_000519045.1:WP_027456929.1 1 MKIVCLDLEGVLVPEIWIEFSKRTGIPELMRTTRDEPDYDKLMTYRLDILRQHKLGLPDIQKVIGEMGP 69 689****************************************************************** PP TIGR02137 70 legavefvdtlreeaqvvilsdtfqefaqplmkqlgfptllchklvvedsdrvkgyqlrqkdqkrkvvk 138 +ega+ f+d lre++qvvilsdtf+efa+plm+qlg+ptl+ch l+ ++ +++ y+lr+ dqkr++vk lcl|NCBI__GCF_000519045.1:WP_027456929.1 70 MEGARAFLDQLREDYQVVILSDTFYEFAHPLMRQLGWPTLFCHSLEDDEQGMLVDYHLRMPDQKREAVK 138 ********************************************************************* PP TIGR02137 139 alkelyykviaagdsyndttmlkeadkgilfhapesvvaefpqleavktyeelkdkflka 198 +kel+++v+aagdsyndt+ml ea+ gilfh pe+v++efpq++ + +y++l+ ++ ka lcl|NCBI__GCF_000519045.1:WP_027456929.1 139 RFKELNFQVVAAGDSYNDTAMLGEAHGGILFHPPENVIREFPQFPVALSYDQLRAEIDKA 198 ******************************************************999886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (203 nodes) Target sequences: 1 (204 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: 00:00:00.00 # Mc/sec: 6.53 // [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