Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_215905524.1 AFE_RS12080 triose-phosphate isomerase
Query= BRENDA::P0A858 (255 letters) >NCBI__GCF_000021485.1:WP_215905524.1 Length = 253 Score = 218 bits (554), Expect = 1e-61 Identities = 124/250 (49%), Positives = 158/250 (63%), Gaps = 3/250 (1%) Query: 5 LVMGNWKLNG-SRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIMLGA 63 +V GNWK+NG S VH + L L + V I PP + +EA+ S + G Sbjct: 1 MVAGNWKMNGLSGDAVHLTQAILHAGLEPMRP-EVVIFPPFTLLHAVSQEAKSSALRWGG 59 Query: 64 QNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTP 123 QN+ SGA+TGE S AML+D+G +Y++IGHSERR ESD I +K GL P Sbjct: 60 QNLFWEASGAYTGEISGAMLRDMGCRYVLIGHSERRQIFAESDAQIVQKIKAALLSGLIP 119 Query: 124 VLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFE-GAVIAYEPVWAIGTGKSATPAQ 182 V+C+GETEAE G T+ V RQ++AVL A + +IAYEPVWAIGTG SA+P Q Sbjct: 120 VVCVGETEAERAQGLTDAVLRRQLEAVLPLLNLEASQPNLIIAYEPVWAIGTGLSASPEQ 179 Query: 183 AQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKADAF 242 AQAVH FIR+ A A +A ++++ YGGSV +NAA LF Q DIDGALVGGASL+A F Sbjct: 180 AQAVHVFIRELAAAYSAQLARRLLLLYGGSVKGNNAAALFDQADIDGALVGGASLQAGEF 239 Query: 243 AVIVKAAEAA 252 I +AAE+A Sbjct: 240 IQICRAAESA 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: 185 Number of extensions: 5 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: 253 Length adjustment: 24 Effective length of query: 231 Effective length of database: 229 Effective search space: 52899 Effective search space used: 52899 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_215905524.1 AFE_RS12080 (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.2549104.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-60 190.4 0.0 2.3e-60 190.3 0.0 1.0 1 NCBI__GCF_000021485.1:WP_215905524.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000021485.1:WP_215905524.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 190.3 0.0 2.3e-60 2.3e-60 1 227 [. 1 236 [. 1 237 [. 0.93 Alignments for each domain: == domain 1 score: 190.3 bits; conditional E-value: 2.3e-60 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 +v +n+K+n+ g+ + + + + ++ ev++ ppf l+ v++e++ s ++ + qn+ sGa+tGe NCBI__GCF_000021485.1:WP_215905524.1 1 MVAGNWKMNGLSGDAVHLTQAILHAGLEPMRPEVVIFPPFTLLHAVSQEAKsSALRWGGQNLFWEASGAYTGE 73 699*******988877777777777779999*******************9889******************* PP TIGR00419 73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartinnv 138 is +ml+d+G+++vligHsErR +++e+d i +k+ + gl +vvCvget++er r++++v NCBI__GCF_000021485.1:WP_215905524.1 74 ISGAMLRDMGCRYVLIGHSERRQIFAESDAQIVQKIKAALLSGLIPVVCVGETEAERAqgltdavLRRQLEAV 146 *********************************************************9888887777899999 PP TIGR00419 139 attaaaaAlepd.vvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaela 210 + + A +p+ ++A+EPv++iGtG ++s+ +a++v+ ++r+ + s+++a+ +lyG+sv+++++a l+ NCBI__GCF_000021485.1:WP_215905524.1 147 LPLLNLEASQPNlIIAYEPVWAIGTGLSASPEQAQAVHVFIRELAAAYSAQLARRLLLLYGGSVKGNNAAALF 219 988888887665278***************************888889************************* PP TIGR00419 211 aqldvdGvLlasavlka 227 q d+dG+L+++a+l+a NCBI__GCF_000021485.1:WP_215905524.1 220 DQADIDGALVGGASLQA 236 ***************97 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 13.62 // [ok]
This GapMind analysis is from Apr 09 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