Align Phosphoserine phosphatase ThrH; PSP; PSPase; EC 3.1.3.3 (characterized)
to candidate WP_011814179.1 HHAL_RS07035 bifunctional phosphoserine phosphatase/homoserine phosphotransferase ThrH
Query= SwissProt::Q9I2Y2 (205 letters) >NCBI__GCF_000015585.1:WP_011814179.1 Length = 202 Score = 234 bits (596), Expect = 1e-66 Identities = 114/202 (56%), Positives = 144/202 (71%) Query: 1 MEIACLDLEGVLVPEIWIAFAEKTGIDALKATTRDIPDYDVLMKQRLRILDEHGLKLGDI 60 M I CLDLEGVLVPEIWI A+ TGIDA +ATTRD+PDY+ LM RL +D HGL L DI Sbjct: 1 MNIVCLDLEGVLVPEIWINLADITGIDAFRATTRDVPDYNELMTMRLADMDRHGLGLADI 60 Query: 61 QEVIATLKPLEGAVEFVDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHKLEIDDSD 120 Q V+A L+PL GA EF+D LR +QV+ILSDTFYEF++PLM QLG+PTL CH LE+ ++ Sbjct: 61 QSVVARLEPLSGAREFLDGLRADYQVIILSDTFYEFARPLMAQLGWPTLFCHSLEVTETG 120 Query: 121 RVVGYQLRQKDPKRQSVIAFKSLYYRVIAAGDSYNDTTMLSEAHAGILFHAPENVIREFP 180 R+ + +R D KRQ+V + + L +RV AAGDSYNDT ML A GI F P + +FP Sbjct: 121 RIADFHIRLADHKRQAVESLRGLNFRVAAAGDSYNDTRMLGAADQGIFFCPPAEIAEQFP 180 Query: 181 QFPAVHTYEDLKREFLKASSRS 202 QFP H Y L++ +A +R+ Sbjct: 181 QFPVTHDYGALRQALDQAFARA 202 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: 154 Number of extensions: 4 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: 202 Length adjustment: 21 Effective length of query: 184 Effective length of database: 181 Effective search space: 33304 Effective search space used: 33304 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_011814179.1 HHAL_RS07035 (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.4454.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-87 278.5 0.0 1.5e-87 278.3 0.0 1.0 1 lcl|NCBI__GCF_000015585.1:WP_011814179.1 HHAL_RS07035 bifunctional phosph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015585.1:WP_011814179.1 HHAL_RS07035 bifunctional phosphoserine phosphatase/homoserine phosphotrans # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 278.3 0.0 1.5e-87 1.5e-87 1 198 [. 1 198 [. 1 202 [] 0.98 Alignments for each domain: == domain 1 score: 278.3 bits; conditional E-value: 1.5e-87 TIGR02137 1 qevvtldlegvlvpeiwiavaektgiddlklttrdipdydvlmkqrlkileeenlklsdiqeviatlkl 69 +++v+ldlegvlvpeiwi +a+ tgid++++ttrd+pdy+ lm rl +++++l l+diq v+a l++ lcl|NCBI__GCF_000015585.1:WP_011814179.1 1 MNIVCLDLEGVLVPEIWINLADITGIDAFRATTRDVPDYNELMTMRLADMDRHGLGLADIQSVVARLEP 69 689****************************************************************** PP TIGR02137 70 legavefvdtlreeaqvvilsdtfqefaqplmkqlgfptllchklvvedsdrvkgyqlrqkdqkrkvvk 138 l ga+ef+d lr ++qv+ilsdtf+efa+plm qlg+ptl+ch l+v ++ r+ +++r d+kr++v lcl|NCBI__GCF_000015585.1:WP_011814179.1 70 LSGAREFLDGLRADYQVIILSDTFYEFARPLMAQLGWPTLFCHSLEVTETGRIADFHIRLADHKRQAVE 138 ********************************************************************* PP TIGR02137 139 alkelyykviaagdsyndttmlkeadkgilfhapesvvaefpqleavktyeelkdkflka 198 +l+ l+++v aagdsyndt ml ad+gi+f+ p ++ +fpq++ ++ y l++ + +a lcl|NCBI__GCF_000015585.1:WP_011814179.1 139 SLRGLNFRVAAAGDSYNDTRMLGAADQGIFFCPPAEIAEQFPQFPVTHDYGALRQALDQA 198 ***************************************************999877665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (203 nodes) Target sequences: 1 (202 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: 00:00:00.00 # Mc/sec: 8.12 // [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