Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_062061912.1 N456_RS21390 triose-phosphate isomerase
Query= BRENDA::P35144 (251 letters) >NCBI__GCF_001401755.1:WP_062061912.1 Length = 250 Score = 225 bits (573), Expect = 8e-64 Identities = 112/249 (44%), Positives = 160/249 (64%) Query: 1 MRKPIIAGNWKMNKVLSEATSFVEEVKGAVPSPESVDSVVCAPALFLDRLVEATKGTDLK 60 MRK I+AGNWKMNK L+E + + E+K + + +V A+ L E + D+K Sbjct: 1 MRKKIVAGNWKMNKNLAETKTLLSELKTNLQKAREAEVIVAPTAVNLYMATEELQQVDIK 60 Query: 61 IGAQNMHFEENGAFTGEVSPVALADLGVNYVILGHSERREMFAETDETVNQKTIAAFKHG 120 + AQNMH ENGA+TGE+S L +GV VILGHSERR F ETDE + K A +H Sbjct: 61 VAAQNMHQAENGAYTGEISADMLKRVGVETVILGHSERRAYFGETDELLASKVSKALQHD 120 Query: 121 LTPIVCCGETNEEYEQDQTKTVVANQVQKALAGLTDEQVKQTVIAYEPIWAIGTGKSSTA 180 +T I C GE ++ + D +V NQ++ L + E K V+AYEP+WAIGTG++++ Sbjct: 121 MTVIFCFGEELQDRKSDNHFAIVENQLKNGLFHINTEDWKNVVLAYEPVWAIGTGETASP 180 Query: 181 EGANEVCAYIRSVVAEQFSQDVADAVRIQYGGSVKPANIKEYMSQSDIDGALVGGASLEA 240 E A E+ A+IR+ +A+ ++Q +AD V I YGGSVKP N E ++ D+DG L+GGASL+A Sbjct: 181 EQAQEMHAFIRNTIAKAYTQQIADEVSILYGGSVKPNNANEIFAKPDVDGGLIGGASLDA 240 Query: 241 DSFLQLLEA 249 +SF+ ++ A Sbjct: 241 ESFVAIVNA 249 Lambda K H 0.313 0.129 0.360 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: 2 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: 251 Length of database: 250 Length adjustment: 24 Effective length of query: 227 Effective length of database: 226 Effective search space: 51302 Effective search space used: 51302 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 46 (22.3 bits)
Align candidate WP_062061912.1 N456_RS21390 (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.496538.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-70 223.8 1.7 1.4e-70 223.6 1.7 1.0 1 NCBI__GCF_001401755.1:WP_062061912.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001401755.1:WP_062061912.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 223.6 1.7 1.4e-70 1.4e-70 1 228 [] 5 241 .. 5 241 .. 0.96 Alignments for each domain: == domain 1 score: 223.6 bits; conditional E-value: 1.4e-70 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 +v +n+K+n + + ++++++l+ ++ + + ev vap v l ++++e++ +i+vaAqn++ + Ga+tGe NCBI__GCF_001401755.1:WP_062061912.1 5 IVAGNWKMNKNLAETKTLLSELKTNLQKAREAEVIVAPTAVNLYMATEELQqVDIKVAAQNMHQAENGAYTGE 77 699***********************************************989******************** PP TIGR00419 73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaaa 145 isA+mlk +G++ v++gHsErR+++ e+del++ kv+++ + +++++ C ge l++r++ +++ v ++ + NCBI__GCF_001401755.1:WP_062061912.1 78 ISADMLKRVGVETVILGHSERRAYFGETDELLASKVSKALQHDMTVIFCFGEELQDRKSDNHFAIVENQLKNG 150 **********************************************************888888887777665 PP TIGR00419 146 A.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaaedaela 210 ++++v+A+EPv++iGtG ++s+ +a+++++++r+ ++k ++++a++v++lyG+sv+ +++ e + NCBI__GCF_001401755.1:WP_062061912.1 151 LfhintedWKNVVLAYEPVWAIGTGETASPEQAQEMHAFIRNTIAKaYTQQIADEVSILYGGSVKPNNANEIF 223 55667788**************************************66899********************** PP TIGR00419 211 aqldvdGvLlasavlkae 228 a++dvdG L+++a+l ae NCBI__GCF_001401755.1:WP_062061912.1 224 AKPDVDGGLIGGASLDAE 241 ***************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (250 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: 15.44 // [ok]
This GapMind analysis is from Sep 24 2021. 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