Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_028313138.1 G491_RS0100105 triose-phosphate isomerase
Query= SwissProt::Q8XKU1 (248 letters) >NCBI__GCF_000429905.1:WP_028313138.1 Length = 253 Score = 251 bits (640), Expect = 1e-71 Identities = 131/249 (52%), Positives = 172/249 (69%), Gaps = 2/249 (0%) Query: 2 RTPIIAGNWKMHYTIDEAVKLVEELKPLVKDAK-CEVVVCPTFVCLDAVKKAVEGTNIKV 60 RTP+IAGNWKM T EA + L LVK + +V++ PTF CL V +A+EG+ + + Sbjct: 4 RTPLIAGNWKMFKTPQEAARDAAALAELVKGVEGVDVMIAPTFACLVPVAQALEGSAVAL 63 Query: 61 GAQNMHFEEKGAFTGEIAPRMLEAMNIDYVIIGHSERREYFNETDETCNKKVKAAFAHNL 120 GAQNMH+E +GA+TGE++ ML+A +VIIGHSERR+YF ETDET NKK+KAA L Sbjct: 64 GAQNMHWETEGAYTGELSGPMLKAAGCSHVIIGHSERRQYFGETDETVNKKIKAALEAGL 123 Query: 121 TPILCCGETLEQRENGTTNDVIKAQITADLEGLTKEQAE-KVVIAYEPIWAIGTGKTATS 179 +LC GET E+R+ T +V+ Q+ L+ + E +V+AYEP+WAIGTGKTAT Sbjct: 124 KAVLCIGETEEERDQEKTLNVLDKQLKDGLKDIFPGSGEDALVVAYEPVWAIGTGKTATD 183 Query: 180 DQANETIAAIRAMVAEMFGQEVADKVRIQYGGSVKPNTIAEQMAKSDIDGALVGGASLVA 239 DQA E A IR ++AE+ G+++A RI YGGSVKP IA+ M+K DIDG LVGGASL Sbjct: 184 DQAQEAHAFIRKVLAELLGKDLAKSTRILYGGSVKPANIAQLMSKPDIDGGLVGGASLDP 243 Query: 240 ADFAQIVNY 248 F+QIV + Sbjct: 244 ETFSQIVKF 252 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: 184 Number of extensions: 11 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: 253 Length adjustment: 24 Effective length of query: 224 Effective length of database: 229 Effective search space: 51296 Effective search space used: 51296 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_028313138.1 G491_RS0100105 (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.12262.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-64 202.2 0.1 6.1e-64 202.0 0.1 1.0 1 lcl|NCBI__GCF_000429905.1:WP_028313138.1 G491_RS0100105 triose-phosphate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429905.1:WP_028313138.1 G491_RS0100105 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 202.0 0.1 6.1e-64 6.1e-64 1 228 [] 7 244 .. 7 244 .. 0.96 Alignments for each domain: == domain 1 score: 202.0 bits; conditional E-value: 6.1e-64 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGa 68 l+ +n+K+ + ++ + a lae v +++gv v +ap f l v++++e s + ++Aqn++ + Ga lcl|NCBI__GCF_000429905.1:WP_028313138.1 7 LIAGNWKMFKTPQEAARDAAALAELVKGVEGVDVMIAPTFACLVPVAQALEgSAVALGAQNMHWETEGA 75 689************************************************9***************** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinn 137 +tGe+s mlk +G+ +v+igHsErR ++ e+de ++kk+ + e glk+v+C+get+eer+ +t+n+ lcl|NCBI__GCF_000429905.1:WP_028313138.1 76 YTGELSGPMLKAAGCSHVIIGHSERRQYFGETDETVNKKIKAALEAGLKAVLCIGETEEERDQEKTLNV 144 ********************************************************************* PP TIGR00419 138 vattaaaaA........lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvly 197 + ++ + + vvA+EPv++iGtGk+++ +a++ ++++r l++ k++a+s+r+ly lcl|NCBI__GCF_000429905.1:WP_028313138.1 145 LDKQLKDGLkdifpgsgEDALVVAYEPVWAIGTGKTATDDQAQEAHAFIRKVLAElLGKDLAKSTRILY 213 *999876656777777667789********************************9999*********** PP TIGR00419 198 GasvtaaedaelaaqldvdGvLlasavlkae 228 G+sv+ a+ a+l+ ++d+dG L+++a+l +e lcl|NCBI__GCF_000429905.1:WP_028313138.1 214 GGSVKPANIAQLMSKPDIDGGLVGGASLDPE 244 ***************************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (253 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: 7.19 // [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