Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_012103713.1 CKL_RS16440 triose-phosphate isomerase
Query= SwissProt::Q8XKU1 (248 letters) >NCBI__GCF_000016505.1:WP_012103713.1 Length = 248 Score = 345 bits (886), Expect = e-100 Identities = 167/248 (67%), Positives = 204/248 (82%) Query: 1 MRTPIIAGNWKMHYTIDEAVKLVEELKPLVKDAKCEVVVCPTFVCLDAVKKAVEGTNIKV 60 MR IIAGNWKM+ +++A++LVEELKPLV+ AKC+VV+CP +VCLDAV K+V GTNIKV Sbjct: 1 MRKAIIAGNWKMNKNLEDALELVEELKPLVRGAKCDVVLCPPYVCLDAVVKSVGGTNIKV 60 Query: 61 GAQNMHFEEKGAFTGEIAPRMLEAMNIDYVIIGHSERREYFNETDETCNKKVKAAFAHNL 120 GAQNMH+EE GA+TGEI+P ML+++ +DYVIIGHSERR+YFNE DET NKK+K AF H++ Sbjct: 61 GAQNMHYEESGAYTGEISPGMLKSLKVDYVIIGHSERRQYFNEKDETINKKIKKAFEHDI 120 Query: 121 TPILCCGETLEQRENGTTNDVIKAQITADLEGLTKEQAEKVVIAYEPIWAIGTGKTATSD 180 PI+CCGE+L +RENG T +V+ QI L+ L KEQ EK+VIAYEPIWAIGTGKTAT Sbjct: 121 IPIVCCGESLLERENGITEEVLGRQIKLALKDLRKEQVEKIVIAYEPIWAIGTGKTATDK 180 Query: 181 QANETIAAIRAMVAEMFGQEVADKVRIQYGGSVKPNTIAEQMAKSDIDGALVGGASLVAA 240 QAN+TIA IR +V++M+G+ A+ VRIQYGGSVKP TI QM + IDGALVGGASL Sbjct: 181 QANDTIAHIRGVVSKMYGENAAEVVRIQYGGSVKPATIKAQMEQPHIDGALVGGASLKPQ 240 Query: 241 DFAQIVNY 248 DFA IVNY Sbjct: 241 DFAAIVNY 248 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: 218 Number of extensions: 5 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: 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_012103713.1 CKL_RS16440 (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.5801.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-59 185.8 0.8 6e-59 185.6 0.8 1.0 1 lcl|NCBI__GCF_000016505.1:WP_012103713.1 CKL_RS16440 triose-phosphate iso Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016505.1:WP_012103713.1 CKL_RS16440 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 185.6 0.8 6e-59 6e-59 1 227 [. 5 239 .. 5 240 .. 0.93 Alignments for each domain: == domain 1 score: 185.6 bits; conditional E-value: 6e-59 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGa 68 ++ +n+K+n +++ ++v +l+ v a++ v++ pp+v ld v++ v ++i+v+Aqn++ +sGa lcl|NCBI__GCF_000016505.1:WP_012103713.1 5 IIAGNWKMNKNLEDALELVEELKPLV-RGAKCDVVLCPPYVCLDAVVKSVGgTNIKVGAQNMHYEESGA 72 6899***************9998655.6689*******************999**************** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinn 137 +tGeis mlk l + +v+igHsErR +++e de i+kk+ ++ e ++ ++vC ge+l ere + t ++ lcl|NCBI__GCF_000016505.1:WP_012103713.1 73 YTGEISPGMLKSLKVDYVIIGHSERRQYFNEKDETINKKIKKAFEHDIIPIVCCGESLLERENGITEEV 141 **************************************************************6666665 PP TIGR00419 138 vattaaaaA.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyG 198 + ++ + a e+ v+A+EP+++iGtGk+++ +a+ + +r ++k ++ ae vr++yG lcl|NCBI__GCF_000016505.1:WP_012103713.1 142 LGRQIKLALkdlrkeqVEKIVIAYEPIWAIGTGKTATDKQANDTIAHIRGVVSKmYGENAAEVVRIQYG 210 5555555545666666************************************9977889999******* PP TIGR00419 199 asvtaaedaelaaqldvdGvLlasavlka 227 +sv+ a + ++ q+ +dG+L+++a+lk+ lcl|NCBI__GCF_000016505.1:WP_012103713.1 211 GSVKPATIKAQMEQPHIDGALVGGASLKP 239 ****************************8 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 6.34 // [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