Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_011840459.1 RSPH17029_RS03035 triose-phosphate isomerase
Query= SwissProt::Q8L1Z5 (254 letters) >NCBI__GCF_000015985.1:WP_011840459.1 Length = 245 Score = 256 bits (655), Expect = 2e-73 Identities = 133/241 (55%), Positives = 174/241 (72%), Gaps = 7/241 (2%) Query: 5 IRPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGGENIL 64 +R AGNWKMNGT LGE+ A+ A + E LIC PATL++R + ++ Sbjct: 1 MRKLAAGNWKMNGTEADLGEIDALLAAHPAPR---CEMLICPPATLVARMAG-RAAQGLM 56 Query: 65 LGGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAAWRAG 124 +GGQ+CH G +TGD+SA ML +AGASHVI+GHSERR + E+D++VR K +AAW AG Sbjct: 57 VGGQDCHPKTSGAHTGDVSAAMLADAGASHVILGHSERRADHGETDSLVRLKAEAAWGAG 116 Query: 125 LVALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTATSAD 184 LVA++CVGET +R + + LDV+ QL GS+P+ ATA N +IAYEPVWA+GTG T T+A+ Sbjct: 117 LVAIVCVGETEAQRDAGQTLDVIGAQLAGSVPEAATAANTVIAYEPVWAIGTGRTPTTAE 176 Query: 185 VAEVHAFIHHKMHSRFGD-EGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLKAID 243 +AEVHAF+ ++ RF D EG RLLYGGSVKPSNA E+ + +V+GAL+GGASLKA D Sbjct: 177 IAEVHAFLRARLAERFSDAEG--FRLLYGGSVKPSNAAEIFAVPNVDGALVGGASLKAAD 234 Query: 244 F 244 F Sbjct: 235 F 235 Lambda K H 0.320 0.137 0.403 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: 256 Number of extensions: 9 Number of successful extensions: 4 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: 254 Length of database: 245 Length adjustment: 24 Effective length of query: 230 Effective length of database: 221 Effective search space: 50830 Effective search space used: 50830 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 bits)
Align candidate WP_011840459.1 RSPH17029_RS03035 (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.carbon/TIGR00419.hmm # target sequence database: /tmp/gapView.38164.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.6e-58 182.0 0.4 8.9e-58 181.8 0.4 1.0 1 NCBI__GCF_000015985.1:WP_011840459.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000015985.1:WP_011840459.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 181.8 0.4 8.9e-58 8.9e-58 3 227 .. 6 232 .. 4 233 .. 0.91 Alignments for each domain: == domain 1 score: 181.8 bits; conditional E-value: 8.9e-58 TIGR00419 3 iinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeveseiqvaAqnvdavksGaftGeisA 75 +n+K+n++ + ++ a la++ a + +e+ + pp + +++ ++ ++v+ q+++ ++sGa+tG++sA NCBI__GCF_000015985.1:WP_011840459.1 6 AGNWKMNGTEADLGEIDALLAAHPAPR--CEMLICPPATLVARMAGRAAQGLMVGGQDCHPKTSGAHTGDVSA 76 69************9999999998876..577888887777766666666*********************** PP TIGR00419 76 emlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaa..... 143 +ml+d+Ga +v++gHsErR+ + e+d l+ k + gl ++vCvget+++r+a++t++++ + a NCBI__GCF_000015985.1:WP_011840459.1 77 AMLADAGASHVILGHSERRADHGETDSLVRLKAEAAWGAGLVAIVCVGETEAQRDAGQTLDVIGAQLAgsvpe 149 ***************************************************************9886523332 PP TIGR00419 144 aaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvd 216 aa + v+A+EPv++iGtG++ + Ae +v++++r l++ + ae r+lyG+sv+ +++ae +a ++vd NCBI__GCF_000015985.1:WP_011840459.1 150 AATAANTVIAYEPVWAIGTGRTPTTAEIAEVHAFLRARLAERFSD-AEGFRLLYGGSVKPSNAAEIFAVPNVD 221 566999******************************888875554.899************************ PP TIGR00419 217 GvLlasavlka 227 G+L+++a+lka NCBI__GCF_000015985.1:WP_011840459.1 222 GALVGGASLKA 232 **********8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (245 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 12.18 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Sep 17 2021.
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