Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate 6936772 Sama_0957 Triose-phosphate isomerase (RefSeq)
Query= BRENDA::P0A858 (255 letters) >FitnessBrowser__SB2B:6936772 Length = 260 Score = 243 bits (620), Expect = 3e-69 Identities = 121/259 (46%), Positives = 170/259 (65%), Gaps = 8/259 (3%) Query: 1 MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAE----- 55 +R P+V GNWK+NGS + EL +L + V + PP +Y++ ++ E Sbjct: 3 LRRPMVAGNWKMNGSAALAQELFKKFAVKLQNDSA-EVVLCPPTIYLESVRQLLEANKEA 61 Query: 56 --GSHIMLGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKF 113 G + +GAQN+ + GA+TGE S MLKD G +Y+I+GHSERR + E+ +++A+KF Sbjct: 62 LNGCLVRMGAQNLSQHDFGAYTGEISGQMLKDSGCRYVIVGHSERRRMYGETSDIVAEKF 121 Query: 114 AVLKEQGLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIG 173 A ++ GLTP+LC+GE+ EA +T EV A ++D V++ G AF+ A+IAYEP+WA+G Sbjct: 122 AAAQKHGLTPILCVGESGPAREARRTFEVIAEELDVVIEKNGTMAFDNAIIAYEPLWAVG 181 Query: 174 TGKSATPAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVG 233 TGKSATP QAQ VH FIR +++V I E V I YGGSV SNAA+LFAQPD+DG L+G Sbjct: 182 TGKSATPEQAQEVHAFIRRRLSEVSPFIGENVRILYGGSVTPSNAADLFAQPDVDGGLIG 241 Query: 234 GASLKADAFAVIVKAAEAA 252 GASL + F + A +A Sbjct: 242 GASLNSTEFLTLCSIAMSA 260 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: 194 Number of extensions: 6 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: 255 Length of database: 260 Length adjustment: 24 Effective length of query: 231 Effective length of database: 236 Effective search space: 54516 Effective search space used: 54516 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 6936772 Sama_0957 (Triose-phosphate isomerase (RefSeq))
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.5770.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.2e-69 217.7 0.0 1.1e-68 217.4 0.0 1.1 1 lcl|FitnessBrowser__SB2B:6936772 Sama_0957 Triose-phosphate isome Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6936772 Sama_0957 Triose-phosphate isomerase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 217.4 0.0 1.1e-68 1.1e-68 1 226 [. 7 246 .. 7 248 .. 0.93 Alignments for each domain: == domain 1 score: 217.4 bits; conditional E-value: 1.1e-68 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdevese........iqvaAqnvdavksGaf 69 +v +n+K+n+s +++ k a ++ + + ev++ pp ++l+ v++ +e++ ++++Aqn+ +++Ga+ lcl|FitnessBrowser__SB2B:6936772 7 MVAGNWKMNGSAALAQELFKKFAVKLQN-DSAEVVLCPPTIYLESVRQLLEANkealngclVRMGAQNLSQHDFGAY 82 699**********************975.66899**********99876553222334444899************* PP TIGR00419 70 tGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartinnva 139 tGeis +mlkd G+++v++gHsErR + e+++++++k+a +++ gl++++Cvge+ re a+++++v lcl|FitnessBrowser__SB2B:6936772 83 TGEISGQMLKDSGCRYVIVGHSERRRMYGETSDIVAEKFAAAQKHGLTPILCVGESGPAREarrtfevIAEELDVVI 159 *************************99999999***********************999998888888899999999 PP TIGR00419 140 ttaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvd 216 ++++++A++++++A+EP +++GtGk++++ +a++v++++r l++vs+ + e+vr+lyG+svt +++a+l+aq+dvd lcl|FitnessBrowser__SB2B:6936772 160 EKNGTMAFDNAIIAYEPLWAVGTGKSATPEQAQEVHAFIRRRLSEVSPFIGENVRILYGGSVTPSNAADLFAQPDVD 236 9**************************************************************************** PP TIGR00419 217 GvLlasavlk 226 G L+++a+l lcl|FitnessBrowser__SB2B:6936772 237 GGLIGGASLN 246 *******996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (260 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.69 // [ok]
This GapMind analysis is from Sep 17 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