Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_092347986.1 BLU87_RS10615 triose-phosphate isomerase
Query= BRENDA::Q6GIL6 (253 letters) >NCBI__GCF_900107645.1:WP_092347986.1 Length = 250 Score = 247 bits (630), Expect = 2e-70 Identities = 122/249 (48%), Positives = 172/249 (69%), Gaps = 2/249 (0%) Query: 1 MRTPIIAGNWKMNKTVQEAKDFVNALPTLPDSKEVESVICAPAIQLDALTTAVKEGKAQG 60 MR P+IAGNWK+NKT+ E++ L + ++ AP AL + K+ Sbjct: 1 MRKPLIAGNWKLNKTINESQQLSRQLLESLGTVSNREIVIAPVFT--ALNAVSEIIKSSS 58 Query: 61 LEIGAQNTYFEDNGAFTGETSPVALADLGVKYVVIGHSERRELFHETDEEINKKAHAIFK 120 + + AQN Y GAFTGE SP+ L D G +YV+IGHSERR+L HET+ IN+K + + Sbjct: 59 ILLAAQNCYPATTGAFTGELSPLFLQDAGCQYVIIGHSERRQLLHETNAFINQKLIGVIQ 118 Query: 121 HGMTPIICVGETDEERESGKANDVVGEQVKKAVAGLSEDQLKSVVIAYEPIWAIGTGKSS 180 G+ PI+C+GET ++RE G+ +++G+Q+K+ + L+ DQ+ +VVIAYEPIWAIGTGK++ Sbjct: 119 AGLKPILCIGETLQQREDGQMLEILGQQIKEGLVDLTTDQMATVVIAYEPIWAIGTGKTA 178 Query: 181 TSEDANEMCAFVRQTIADLSSKEVSEATRIQYGGSVKPNNIKEYMAQTDIDGALVGGASL 240 +SE A E A++R + ++ + V+E TRI YGGSVKP+NI MAQTDIDGALVGGASL Sbjct: 179 SSEQAQEAHAYIRSLLQEIFNSSVAEQTRILYGGSVKPDNIDTLMAQTDIDGALVGGASL 238 Query: 241 KVEDFVQLL 249 K EDFV+++ Sbjct: 239 KAEDFVRIV 247 Lambda K H 0.311 0.129 0.359 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: 201 Number of extensions: 6 Number of successful extensions: 2 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: 253 Length of database: 250 Length adjustment: 24 Effective length of query: 229 Effective length of database: 226 Effective search space: 51754 Effective search space used: 51754 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 46 (22.3 bits)
Align candidate WP_092347986.1 BLU87_RS10615 (triose-phosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))
# 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/TIGR00419.hmm # target sequence database: /tmp/gapView.5393.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00419 [M=228] Accession: TIGR00419 Description: tim: triose-phosphate isomerase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.4e-66 207.9 0.2 1.1e-65 207.7 0.2 1.0 1 lcl|NCBI__GCF_900107645.1:WP_092347986.1 BLU87_RS10615 triose-phosphate i Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900107645.1:WP_092347986.1 BLU87_RS10615 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 207.7 0.2 1.1e-65 1.1e-65 1 228 [] 5 241 .. 5 241 .. 0.95 Alignments for each domain: == domain 1 score: 207.7 bits; conditional E-value: 1.1e-65 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGa 68 l+ +n+Kln ++++ +++ +l e + +++ e+++ap f l+ v++ ++ s i +aAqn+ ++Ga lcl|NCBI__GCF_900107645.1:WP_092347986.1 5 LIAGNWKLNKTINESQQLSRQLLESLGTVSNREIVIAPVFTALNAVSEIIKsSSILLAAQNCYPATTGA 73 689***********************************************9899*************** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinn 137 ftGe+s l+d+G+++v+igHsErR ll+e++ +i++k+ + + glk+++C+getl++re ++ ++ lcl|NCBI__GCF_900107645.1:WP_092347986.1 74 FTGELSPLFLQDAGCQYVIIGHSERRQLLHETNAFINQKLIGVIQAGLKPILCIGETLQQREDGQMLEI 142 **************************************************************8888887 PP TIGR00419 138 vattaaaaA.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyG 198 + ++ + + +v+A+EP+++iGtGk++s +a++ ++ +r l++ + vae++r+lyG lcl|NCBI__GCF_900107645.1:WP_092347986.1 143 LGQQIKEGLvdlttdqMATVVIAYEPIWAIGTGKTASSEQAQEAHAYIRSLLQEiFNSSVAEQTRILYG 211 77665543345666668999********************************997899*********** PP TIGR00419 199 asvtaaedaelaaqldvdGvLlasavlkae 228 +sv+ + l+aq d+dG+L+++a+lkae lcl|NCBI__GCF_900107645.1:WP_092347986.1 212 GSVKPDNIDTLMAQTDIDGALVGGASLKAE 241 ****************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (250 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: 6.77 // [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