Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate HSERO_RS08805 HSERO_RS08805 triosephosphate isomerase
Query= BRENDA::P0A858 (255 letters) >FitnessBrowser__HerbieS:HSERO_RS08805 Length = 238 Score = 210 bits (535), Expect = 2e-59 Identities = 111/238 (46%), Positives = 147/238 (61%), Gaps = 1/238 (0%) Query: 12 LNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIMLGAQNVDLNLS 71 +NGS LV+ +++ LA A C VA+ P Y+ + GS + LGAQ++ + S Sbjct: 1 MNGSLAANAALVAGIKEGLAAQA-CDVAVCVPAPYLAQVQALVAGSPVGLGAQDMSAHAS 59 Query: 72 GAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTPVLCIGETE 131 GA+TGE SA+ML++ G QY+I+GHSERR YH ESD +A K + GL P++C+GET Sbjct: 60 GAYTGEVSASMLQEFGVQYVILGHSERRAYHGESDAAVAAKTVAALKAGLVPLVCVGETL 119 Query: 132 AENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATPAQAQAVHKFIR 191 + EAG+T V Q+D VL A V+AYEPVWAIGTGK+ATP AQ VH +R Sbjct: 120 EQREAGQTNAVVGGQLDVVLAALSAEEAARIVVAYEPVWAIGTGKTATPEMAQEVHAMLR 179 Query: 192 DHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKADAFAVIVKAA 249 + A A +V I YGGS+ NA +L A DIDG L+GGA+LKA F I+ AA Sbjct: 180 ARLGAKSAEAAAKVCILYGGSMKPDNAQQLLAMGDIDGGLIGGAALKAADFLAIINAA 237 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: 184 Number of extensions: 6 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: 238 Length adjustment: 24 Effective length of query: 231 Effective length of database: 214 Effective search space: 49434 Effective search space used: 49434 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 HSERO_RS08805 HSERO_RS08805 (triosephosphate 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.16163.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-58 182.7 8.6 5.3e-58 182.5 8.6 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS08805 HSERO_RS08805 triosephosphate is Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS08805 HSERO_RS08805 triosephosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 182.5 8.6 5.3e-58 5.3e-58 9 227 .. 2 227 .. 1 228 [. 0.94 Alignments for each domain: == domain 1 score: 182.5 bits; conditional E-value: 5.3e-58 TIGR00419 9 nesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGeisA 75 n+s+ + +va ++e +a + + vav +p +l v+ v s + ++Aq++ a+ sGa+tGe+sA lcl|FitnessBrowser__HerbieS:HSERO_RS08805 2 NGSLAANAALVAGIKEGLAAQ-ACDVAVCVPAPYLAQVQALVAgSPVGLGAQDMSAHASGAYTGEVSA 68 8999999**********9976.58999999999********99999********************** PP TIGR00419 76 emlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartin 136 ml+++G+++v++gHsErR+++ e+d +++k + + gl ++vCvgetle+re ++ +++ lcl|FitnessBrowser__HerbieS:HSERO_RS08805 69 SMLQEFGVQYVILGHSERRAYHGESDAAVAAKTVAALKAGLVPLVCVGETLEQREagqtnavVGGQLD 136 ********************************999999*****************7776666667777 PP TIGR00419 137 nvattaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaa 204 +v+ +a vvA+EPv++iGtGk++++ a++v++++r l s+e a +v +lyG+s++ lcl|FitnessBrowser__HerbieS:HSERO_RS08805 137 VVLAALSAEEAARIVVAYEPVWAIGTGKTATPEMAQEVHAMLRARLGAKSAEAAAKVCILYGGSMKPD 204 77777777778999****************************************************** PP TIGR00419 205 edaelaaqldvdGvLlasavlka 227 ++++l a d+dG L+++a lka lcl|FitnessBrowser__HerbieS:HSERO_RS08805 205 NAQQLLAMGDIDGGLIGGAALKA 227 **********************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (238 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: 6.55 // [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