Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_013537411.1 THEAM_RS03325 triose-phosphate isomerase
Query= SwissProt::Q8XKU1 (248 letters) >NCBI__GCF_000185805.1:WP_013537411.1 Length = 248 Score = 268 bits (685), Expect = 8e-77 Identities = 140/247 (56%), Positives = 175/247 (70%), Gaps = 3/247 (1%) Query: 1 MRTPIIAGNWKMHYTIDEAVKLVEELKPLVKDAKC-EVVVCPTFVCLDAVKKAVEGTNIK 59 MR +IAGNWKMH T+ EAV+LV ELK LVKD +++VCP F L V + ++G+NI Sbjct: 1 MRRLLIAGNWKMHKTVPEAVELVRELKELVKDVTDRDILVCPPFTALYPVSQELKGSNIY 60 Query: 60 VGAQNMHFEEKGAFTGEIAPRMLEAMNIDYVIIGHSERREYFNETDETCNKKVKAAFAHN 119 +G QNM +EE+GAFTGEI+P ML+ + +VI+GHSERR F E D NKKV +A H Sbjct: 61 LGGQNMFYEEEGAFTGEISPLMLKDVGCRFVILGHSERRHIFKEDDRLINKKVLSAVEHG 120 Query: 120 LTPILCCGETLEQRENGTTNDVIKAQITADLEGLTKEQAEKVVIAYEPIWAIGTGKTATS 179 LTPILC GETL++RE+G T +V+K Q+ L+GLT E + VIAYEP+WAIGTG+TAT Sbjct: 121 LTPILCVGETLQERESGRTKEVVKKQVVEGLKGLTPE--SEFVIAYEPVWAIGTGRTATP 178 Query: 180 DQANETIAAIRAMVAEMFGQEVADKVRIQYGGSVKPNTIAEQMAKSDIDGALVGGASLVA 239 + A E IR + E+FG E A+ VRI YGGSVKPN A + DIDGALVGGASL A Sbjct: 179 ELAQEVHEFIRNTLKELFGSEKAETVRILYGGSVKPNNAAGLLKMPDIDGALVGGASLKA 238 Query: 240 ADFAQIV 246 F+QIV Sbjct: 239 ESFSQIV 245 Lambda K H 0.316 0.131 0.376 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: 177 Number of extensions: 5 Number of successful extensions: 3 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: 248 Length of database: 248 Length adjustment: 24 Effective length of query: 224 Effective length of database: 224 Effective search space: 50176 Effective search space used: 50176 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 46 (22.3 bits)
Align candidate WP_013537411.1 THEAM_RS03325 (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.11133.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-67 212.0 0.0 6e-67 211.8 0.0 1.0 1 lcl|NCBI__GCF_000185805.1:WP_013537411.1 THEAM_RS03325 triose-phosphate i Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000185805.1:WP_013537411.1 THEAM_RS03325 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 211.8 0.0 6e-67 6e-67 1 228 [] 5 239 .. 5 239 .. 0.95 Alignments for each domain: == domain 1 score: 211.8 bits; conditional E-value: 6e-67 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGa 68 l+ +n+K++ +v + ++v +l+e v ++++ + v ppf l v++e++ s+i ++ qn+ + Ga lcl|NCBI__GCF_000185805.1:WP_013537411.1 5 LIAGNWKMHKTVPEAVELVRELKELVKDVTDRDILVCPPFTALYPVSQELKgSNIYLGGQNMFYEEEGA 73 689****************************************************************** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinn 137 ftGeis mlkd+G+++v++gHsErR ++ke d li+kkv + e gl++++Cvgetl+ere++rt ++ lcl|NCBI__GCF_000185805.1:WP_013537411.1 74 FTGEISPLMLKDVGCRFVILGHSERRHIFKEDDRLINKKVLSAVEHGLTPILCVGETLQERESGRTKEV 142 ********************************************************************9 PP TIGR00419 138 vatt..aaaaAlepd...vvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGas 200 v+++ ++ l+p+ v+A+EPv++iGtG+++++ a++v++++r+ lk+ e ae vr+lyG+s lcl|NCBI__GCF_000185805.1:WP_013537411.1 143 VKKQvvEGLKGLTPEsefVIAYEPVWAIGTGRTATPELAQEVHEFIRNTLKElFGSEKAETVRILYGGS 211 99983323344554333399********************************8899************* PP TIGR00419 201 vtaaedaelaaqldvdGvLlasavlkae 228 v+ +++a l +d+dG+L+++a+lkae lcl|NCBI__GCF_000185805.1:WP_013537411.1 212 VKPNNAAGLLKMPDIDGALVGGASLKAE 239 **************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (248 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: 9.24 // [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