Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_041376588.1 PNAP_RS07095 triose-phosphate isomerase
Query= BRENDA::P0A858 (255 letters) >NCBI__GCF_000015505.1:WP_041376588.1 Length = 252 Score = 235 bits (600), Expect = 6e-67 Identities = 125/249 (50%), Positives = 167/249 (67%), Gaps = 6/249 (2%) Query: 5 LVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYI----DMAKREAEGSHIM 60 L+ GNWK+NGS EL++ L LA C +A+ P Y+ + + A S + Sbjct: 4 LIAGNWKMNGSLTANEELLAALAAGLAQSPPCEIAVCVPAPYLAQIQSLKSKHAALSVVD 63 Query: 61 LGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQG 120 +GAQ+V + SGA+TGE SAAMLK++G +Y+IIGHSERR YH E+D L+A+K G Sbjct: 64 VGAQDVSAHASGAYTGEASAAMLKELGCRYVIIGHSERRQYHAETDALVAEKARAALAAG 123 Query: 121 LTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATP 180 +TP++C+GET E EAG+TEEV RQ+ AV+ G E V+AYEPVWAIGTGK+A+P Sbjct: 124 ITPIVCVGETLTEREAGRTEEVVKRQLAAVIHANGHCISE-IVVAYEPVWAIGTGKTASP 182 Query: 181 AQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKAD 240 +AQAVH +R + K + + ++ I YGGS+NA+NAA L AQPDIDG L+GGASLKA Sbjct: 183 EEAQAVHAVLRAQL-KAATDQSARIKILYGGSMNAANAATLLAQPDIDGGLIGGASLKAP 241 Query: 241 AFAVIVKAA 249 F I+ AA Sbjct: 242 DFLKIIAAA 250 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: 191 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: 255 Length of database: 252 Length adjustment: 24 Effective length of query: 231 Effective length of database: 228 Effective search space: 52668 Effective search space used: 52668 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: 47 (22.7 bits)
Align candidate WP_041376588.1 PNAP_RS07095 (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.27497.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-71 226.5 5.2 2.2e-71 226.3 5.2 1.0 1 lcl|NCBI__GCF_000015505.1:WP_041376588.1 PNAP_RS07095 triose-phosphate is Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015505.1:WP_041376588.1 PNAP_RS07095 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 226.3 5.2 2.2e-71 2.2e-71 1 227 [. 4 240 .. 4 241 .. 0.93 Alignments for each domain: == domain 1 score: 226.3 bits; conditional E-value: 2.2e-71 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvk...deve..seiqvaAqnvdav 64 l+ +n+K+n+s+ e+++a la+ +a++ +e+av +p +l ++ + s ++v+Aq+v a+ lcl|NCBI__GCF_000015505.1:WP_041376588.1 4 LIAGNWKMNGSLTANEELLAALAAGLAQSPPCEIAVCVPAPYLAQIQslkSKHAalSVVDVGAQDVSAH 72 689********************************999998888775221222225889********** PP TIGR00419 65 ksGaftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaar 133 sGa+tGe sA+mlk+lG+++v+igHsErR +++e+d l+++k + + g++++vCvgetl erea+r lcl|NCBI__GCF_000015505.1:WP_041376588.1 73 ASGAYTGEASAAMLKELGCRYVIIGHSERRQYHAETDALVAEKARAALAAGITPIVCVGETLTEREAGR 141 ********************************************************************* PP TIGR00419 134 tinnvattaaaaA......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvl 196 t ++v+++ aa+ +++ vvA+EPv++iGtGk++s+ ea++v++ +r lk ++ + + +++l lcl|NCBI__GCF_000015505.1:WP_041376588.1 142 TEEVVKRQLAAVIhanghcISEIVVAYEPVWAIGTGKTASPEEAQAVHAVLRAQLKAATDQ-SARIKIL 209 *******999987789999999******************************888766655.668**** PP TIGR00419 197 yGasvtaaedaelaaqldvdGvLlasavlka 227 yG+s++aa++a l aq+d+dG L+++a+lka lcl|NCBI__GCF_000015505.1:WP_041376588.1 210 YGGSMNAANAATLLAQPDIDGGLIGGASLKA 240 ******************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (252 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: 5.92 // [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