Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_079557872.1 CDL62_RS17580 triose-phosphate isomerase
Query= SwissProt::Q8XKU1 (248 letters) >NCBI__GCF_002201795.1:WP_079557872.1 Length = 251 Score = 224 bits (570), Expect = 2e-63 Identities = 113/248 (45%), Positives = 157/248 (63%), Gaps = 2/248 (0%) Query: 1 MRTPIIAGNWKMHYTIDEAVKLVEELKPLVK--DAKCEVVVCPTFVCLDAVKKAVEGTNI 58 MR I+AGNWKM+ T+ E ++L +++ V KC+VV+ F+ + V V+G + Sbjct: 1 MRQNIVAGNWKMNKTLQEGIELAKDVNQRVNAITPKCKVVLGTPFIHITEVVNVVDGDKV 60 Query: 59 KVGAQNMHFEEKGAFTGEIAPRMLEAMNIDYVIIGHSERREYFNETDETCNKKVKAAFAH 118 V AQN + GA+TGE++ M+++ YVI+GHSERR Y+ ET+ +K A A+ Sbjct: 61 AVAAQNCADKVSGAYTGEVSAEMVKSTGAAYVILGHSERRAYYGETNAILKEKTDLALAN 120 Query: 119 NLTPILCCGETLEQRENGTTNDVIKAQITADLEGLTKEQAEKVVIAYEPIWAIGTGKTAT 178 NL PI C GE L +RE T DV+K+QI L L+ + K+V+AYEP+WAIGTGKTA+ Sbjct: 121 NLRPIFCIGEVLSEREANTHFDVVKSQIKEALFHLSADDFGKIVLAYEPVWAIGTGKTAS 180 Query: 179 SDQANETIAAIRAMVAEMFGQEVADKVRIQYGGSVKPNTIAEQMAKSDIDGALVGGASLV 238 SDQA E A IR ++ + +G+EVAD + I YGGS P E A D+DG L+GGASL Sbjct: 181 SDQAQEMHAFIRGLITDKYGKEVADNISILYGGSCNPKNAQELFANPDVDGGLIGGASLK 240 Query: 239 AADFAQIV 246 A DF I+ Sbjct: 241 AEDFLAII 248 Lambda K H 0.316 0.131 0.376 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: 165 Number of extensions: 3 Number of successful extensions: 2 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: 248 Length of database: 251 Length adjustment: 24 Effective length of query: 224 Effective length of database: 227 Effective search space: 50848 Effective search space used: 50848 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_079557872.1 CDL62_RS17580 (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.816333.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-65 207.1 1.5 1.9e-65 206.9 1.5 1.0 1 NCBI__GCF_002201795.1:WP_079557872.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002201795.1:WP_079557872.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 206.9 1.5 1.9e-65 1.9e-65 1 228 [] 5 242 .. 5 242 .. 0.96 Alignments for each domain: == domain 1 score: 206.9 bits; conditional E-value: 1.9e-65 TIGR00419 1 lviinfKlnesvgkvelevaklaeevas.eagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftG 71 +v +n+K+n ++++ ++ ++++ v + +++v++ pf+++ v++ v+ ++ vaAqn+ + sGa+tG NCBI__GCF_002201795.1:WP_079557872.1 5 IVAGNWKMNKTLQEGIELAKDVNQRVNAiTPKCKVVLGTPFIHITEVVNVVDgDKVAVAAQNCADKVSGAYTG 77 699***********9999999***99651669********************999****************** PP TIGR00419 72 eisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaa 144 e+sAem+k +Ga++v++gHsErR++ e++ ++++k + + +l+++ C+ge l+erea +++++v+ + + NCBI__GCF_002201795.1:WP_079557872.1 78 EVSAEMVKSTGAAYVILGHSERRAYYGETNAILKEKTDLALANNLRPIFCIGEVLSEREANTHFDVVKSQIKE 150 *******************************************************************999888 PP TIGR00419 145 aA.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaaedael 209 a + + v+A+EPv++iGtGk++s +a+++++++r ++ keva+++++lyG+s + ++++el NCBI__GCF_002201795.1:WP_079557872.1 151 ALfhlsaddFGKIVLAYEPVWAIGTGKTASSDQAQEMHAFIRGLITDkYGKEVADNISILYGGSCNPKNAQEL 223 77788889999*******************************99987699*********************** PP TIGR00419 210 aaqldvdGvLlasavlkae 228 +a++dvdG L+++a+lkae NCBI__GCF_002201795.1:WP_079557872.1 224 FANPDVDGGLIGGASLKAE 242 *****************97 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 21.09 // [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