Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_090445728.1 BLS63_RS14430 triose-phosphate isomerase
Query= BRENDA::P0A858 (255 letters) >NCBI__GCF_900100495.1:WP_090445728.1 Length = 251 Score = 238 bits (606), Expect = 1e-67 Identities = 127/250 (50%), Positives = 165/250 (66%), Gaps = 2/250 (0%) Query: 1 MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM 60 MR PLV GNWK++G+R V EL++ LR +LA +G VA+ P ++I G + Sbjct: 1 MRRPLVAGNWKMHGTRASVAELINGLR-QLAMPSGVEVAVFPGCLHIRQVVEGLTGMRMA 59 Query: 61 LGAQNVDLN-LSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQ 119 +GAQ+ L+ GA TGE +A+ L+D G + +++GHSERR ESDE + +KFA + Sbjct: 60 VGAQDCALDPAQGALTGEVAASQLQDAGCRLVLVGHSERRLLLGESDEWVVRKFAAAQSC 119 Query: 120 GLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSAT 179 L PVLC+GET + EAGKT EV RQ+ +V++ G F AV+AYEPVWAIGTG +A+ Sbjct: 120 SLIPVLCVGETLEQREAGKTLEVVGRQVGSVVEALGVEVFARAVVAYEPVWAIGTGLTAS 179 Query: 180 PAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKA 239 P QAQ +H IR +A DA +A V I YGGSV A+NAAELF PDIDG LVGGASL A Sbjct: 180 PEQAQEIHAAIRAQLAAKDAEVARGVRILYGGSVKAANAAELFGMPDIDGGLVGGASLNA 239 Query: 240 DAFAVIVKAA 249 D F I +AA Sbjct: 240 DEFGAICRAA 249 Lambda K H 0.316 0.130 0.366 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: 178 Number of extensions: 4 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: 255 Length of database: 251 Length adjustment: 24 Effective length of query: 231 Effective length of database: 227 Effective search space: 52437 Effective search space used: 52437 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_090445728.1 BLS63_RS14430 (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.22981.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-69 219.1 1.7 4e-69 218.9 1.7 1.0 1 lcl|NCBI__GCF_900100495.1:WP_090445728.1 BLS63_RS14430 triose-phosphate i Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900100495.1:WP_090445728.1 BLS63_RS14430 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 218.9 1.7 4e-69 4e-69 1 228 [] 5 240 .. 5 240 .. 0.96 Alignments for each domain: == domain 1 score: 218.9 bits; conditional E-value: 4e-69 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdav.ksG 67 lv +n+K+++++ +v+++++ l+ ++a ++gvevav p ++++ v++ + ++ v+Aq++ + +G lcl|NCBI__GCF_900100495.1:WP_090445728.1 5 LVAGNWKMHGTRASVAELINGLR-QLAMPSGVEVAVFPGCLHIRQVVEGLTgMRMAVGAQDCALDpAQG 72 799******************97.7*************************9899********997368* PP TIGR00419 68 aftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartin 136 a tGe+ A l+d+G++ vl+gHsErR ll e+de + k+a ++ l +v+Cvgetle+rea++t++ lcl|NCBI__GCF_900100495.1:WP_090445728.1 73 ALTGEVAASQLQDAGCRLVLVGHSERRLLLGESDEWVVRKFAAAQSCSLIPVLCVGETLEQREAGKTLE 141 ***************************************************************999999 PP TIGR00419 137 nvattaaaaA.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyG 198 +v ++ + + + +vvA+EPv++iGtG ++s+ +a+++++ +r l+ ++eva+ vr+lyG lcl|NCBI__GCF_900100495.1:WP_090445728.1 142 VVGRQVGSVVealgvevFARAVVAYEPVWAIGTGLTASPEQAQEIHAAIRAQLAAKDAEVARGVRILYG 210 99999887767788888**************************************************** PP TIGR00419 199 asvtaaedaelaaqldvdGvLlasavlkae 228 +sv+aa++ael+ +d+dG L+++a+l a+ lcl|NCBI__GCF_900100495.1:WP_090445728.1 211 GSVKAANAAELFGMPDIDGGLVGGASLNAD 240 ***************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (251 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: 10.62 // [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