Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_012971614.1 ALVIN_RS12145 triose-phosphate isomerase
Query= BRENDA::P0A858 (255 letters) >NCBI__GCF_000025485.1:WP_012971614.1 Length = 253 Score = 267 bits (682), Expect = 2e-76 Identities = 132/252 (52%), Positives = 173/252 (68%) Query: 1 MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM 60 MR PL+ GNWK+NG+R L+ + + +G+A +A+ P +++++A+R G I Sbjct: 1 MRQPLIAGNWKMNGTRSSAESLIQGVLEGSSGIAKAEIAVCVPFVFLELAQRLLSGRSIR 60 Query: 61 LGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQG 120 LGAQNV SGA+TGETSA ML + G +Y+I GHSERR Y+ E+D ++AKK A++ G Sbjct: 61 LGAQNVCTEASGAYTGETSAEMLNEFGCRYVICGHSERREYYGETDAIVAKKLAMVASTG 120 Query: 121 LTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATP 180 +TP+LC+GET + E G E V A QIDA+++ G +F IAYEPVWAIGTGK+ATP Sbjct: 121 MTPILCVGETLEQREQGFMEAVIAGQIDAIIEANGIESFGQVAIAYEPVWAIGTGKTATP 180 Query: 181 AQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKAD 240 QAQ VH FIR +A DA IAE+V I YGGS+ SNAAEL A PDIDG L+GGASL A+ Sbjct: 181 EQAQEVHAFIRRRVAAHDAAIAEKVRILYGGSMKPSNAAELLAMPDIDGGLIGGASLVAE 240 Query: 241 AFAVIVKAAEAA 252 F I +A E A Sbjct: 241 DFLAICQAGETA 252 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: 202 Number of extensions: 3 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: 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_012971614.1 ALVIN_RS12145 (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.17801.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-73 232.1 1.4 4.3e-73 231.9 1.4 1.0 1 lcl|NCBI__GCF_000025485.1:WP_012971614.1 ALVIN_RS12145 triose-phosphate i Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025485.1:WP_012971614.1 ALVIN_RS12145 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 231.9 1.4 4.3e-73 4.3e-73 1 228 [] 5 240 .. 5 240 .. 0.99 Alignments for each domain: == domain 1 score: 231.9 bits; conditional E-value: 4.3e-73 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGa 68 l+ +n+K+n+++++ e +++ + e ++ a+ e+av +pfv+l+ +++ ++ i+++Aqnv + sGa lcl|NCBI__GCF_000025485.1:WP_012971614.1 5 LIAGNWKMNGTRSSAESLIQGVLEGSSGIAKAEIAVCVPFVFLELAQRLLSgRSIRLGAQNVCTEASGA 73 689************************************************899*************** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere....... 130 +tGe+sAeml+++G+++v+ gHsErR + e+d +++kk+a++ g+++++Cvgetle+re lcl|NCBI__GCF_000025485.1:WP_012971614.1 74 YTGETSAEMLNEFGCRYVICGHSERREYYGETDAIVAKKLAMVASTGMTPILCVGETLEQREqgfmeav 142 *******************************************************************99 PP TIGR00419 131 aartinnvattaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGa 199 a +i+++ + +++ + ++ +A+EPv++iGtGk++++ +a++v++++r ++ ++ +ae+vr+lyG+ lcl|NCBI__GCF_000025485.1:WP_012971614.1 143 IAGQIDAIIEANGIESFGQVAIAYEPVWAIGTGKTATPEQAQEVHAFIRRRVAAHDAAIAEKVRILYGG 211 999****************************************************************** PP TIGR00419 200 svtaaedaelaaqldvdGvLlasavlkae 228 s++ +++ael a +d+dG L+++a+l ae lcl|NCBI__GCF_000025485.1:WP_012971614.1 212 SMKPSNAAELLAMPDIDGGLIGGASLVAE 240 **************************986 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.47 // [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