Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate 7023804 Shewana3_1026 triosephosphate isomerase (RefSeq)
Query= BRENDA::P0A858 (255 letters) >FitnessBrowser__ANA3:7023804 Length = 260 Score = 246 bits (627), Expect = 4e-70 Identities = 124/259 (47%), Positives = 172/259 (66%), Gaps = 8/259 (3%) Query: 1 MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDM------AKREA 54 +R P+V GNWK+NGS + EL +L + V + PP +Y++ A +EA Sbjct: 3 LRRPMVAGNWKMNGSAALAQELFKKFASKLQNDSA-EVVLCPPSIYLESVRQLLEANKEA 61 Query: 55 -EGSHIMLGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKF 113 +GS + +GAQN+ + GA+TGE S MLKD G +Y+IIGHSERR + E+ ++A+KF Sbjct: 62 LDGSLVRMGAQNLSQHDFGAYTGEVSGQMLKDCGCRYVIIGHSERRRMYGETSNIVAEKF 121 Query: 114 AVLKEQGLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIG 173 A ++ GLTP+LC+GE+ EA +T EV A ++D V++ G AF+ A+IAYEP+WA+G Sbjct: 122 AAAQKHGLTPILCVGESGPAREARRTFEVIAEELDIVIQKNGTMAFDNAIIAYEPLWAVG 181 Query: 174 TGKSATPAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVG 233 TGKSATP QAQ VH FIR +++V I E + I YGGSV SNAA+LFAQPD+DG L+G Sbjct: 182 TGKSATPEQAQEVHAFIRKRLSEVSPFIGENIRILYGGSVTPSNAADLFAQPDVDGGLIG 241 Query: 234 GASLKADAFAVIVKAAEAA 252 GASL + F + A +A Sbjct: 242 GASLNSTEFLSLCTIAMSA 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: 202 Number of extensions: 9 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 7023804 Shewana3_1026 (triosephosphate 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.23258.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-69 218.8 0.0 5.4e-69 218.5 0.0 1.1 1 lcl|FitnessBrowser__ANA3:7023804 Shewana3_1026 triosephosphate is Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7023804 Shewana3_1026 triosephosphate isomerase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 218.5 0.0 5.4e-69 5.4e-69 1 226 [. 7 246 .. 7 248 .. 0.92 Alignments for each domain: == domain 1 score: 218.5 bits; conditional E-value: 5.4e-69 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdevese........iqvaAqnvdavksGaf 69 +v +n+K+n+s +++ k a ++ + + ev++ pp ++l+ v++ +e++ ++++Aqn+ +++Ga+ lcl|FitnessBrowser__ANA3:7023804 7 MVAGNWKMNGSAALAQELFKKFASKLQN-DSAEVVLCPPSIYLESVRQLLEANkealdgslVRMGAQNLSQHDFGAY 82 699**********************976.66899*********99976544221233333399************** PP TIGR00419 70 tGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartinnva 139 tGe+s +mlkd+G+++v+igHsErR + e+++++++k+a +++ gl++++Cvge+ re a++++ v lcl|FitnessBrowser__ANA3:7023804 83 TGEVSGQMLKDCGCRYVIIGHSERRRMYGETSNIVAEKFAAAQKHGLTPILCVGESGPAREarrtfevIAEELDIVI 159 ********************************************************999997777877788888899 PP TIGR00419 140 ttaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvd 216 ++++++A++++++A+EP +++GtGk++++ +a++v++++r l++vs+ + e++r+lyG+svt +++a+l+aq+dvd lcl|FitnessBrowser__ANA3:7023804 160 QKNGTMAFDNAIIAYEPLWAVGTGKSATPEQAQEVHAFIRKRLSEVSPFIGENIRILYGGSVTPSNAADLFAQPDVD 236 999999*********************************************************************** PP TIGR00419 217 GvLlasavlk 226 G L+++a+l lcl|FitnessBrowser__ANA3:7023804 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.41 // [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