Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate RR42_RS05495 RR42_RS05495 triosephosphate isomerase
Query= SwissProt::Q5SJR1 (250 letters) >FitnessBrowser__Cup4G11:RR42_RS05495 Length = 245 Score = 228 bits (582), Expect = 7e-65 Identities = 124/245 (50%), Positives = 159/245 (64%), Gaps = 3/245 (1%) Query: 1 MRRVLVAGNWKMHKTPSEARVWFAELKRLLPPLQSEAAVLPAFPILPVAKEVLAETQVGY 60 MR+ LV GNWKMH + + +K P + AV FP L + +LA + V + Sbjct: 1 MRQKLVIGNWKMHGSLAANVTLLEAIKAA--PASARLAVCAPFPYLAQCQALLAGSAVAW 58 Query: 61 GAQDVSAHKEGAYTGEVSARMLSDLGCRYAIVGHSERRRYHGETDALVAEKAKRLLEEGI 120 GAQDVSA GA+TGEV+A ML++ G YA+VGHSERR YHGETDA VA KA R LE GI Sbjct: 59 GAQDVSAEARGAFTGEVAASMLAEFGASYALVGHSERRSYHGETDATVAAKAVRALEFGI 118 Query: 121 TPILCVGEPLEVREKGEAVPYTLRQLRGSLEGVEPPGPEALVIAYEPVWAIGTGKNATPE 180 P++CVGE L RE GE RQL LE + +V+AYEPVWAIGTGK A+ E Sbjct: 119 VPVVCVGESLAQREAGETEAVVGRQLGAVLEALSLDQLGRIVLAYEPVWAIGTGKTASSE 178 Query: 181 DAEAMHQAIRKALSERYGEAFASRVRILYGGSVNPKNFADLLSMPNVDGGLVGGASLELE 240 A+A+H +R ++ R A+R+ +LYGGSV P N A+L SMP++DGGL+GGASL+ + Sbjct: 179 QAQAVHAFLRAQVAAR-DAGVAARMAMLYGGSVKPDNAAELFSMPDIDGGLIGGASLKSD 237 Query: 241 SFLAL 245 FLA+ Sbjct: 238 DFLAI 242 Lambda K H 0.317 0.135 0.393 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: 185 Number of extensions: 7 Number of successful extensions: 3 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: 250 Length of database: 245 Length adjustment: 24 Effective length of query: 226 Effective length of database: 221 Effective search space: 49946 Effective search space used: 49946 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 RR42_RS05495 RR42_RS05495 (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.32391.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.7e-62 195.3 1.2 7.6e-62 195.1 1.2 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS05495 RR42_RS05495 triosephosphate iso Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS05495 RR42_RS05495 triosephosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 195.1 1.2 7.6e-62 7.6e-62 1 228 [] 5 237 .. 5 237 .. 0.93 Alignments for each domain: == domain 1 score: 195.1 bits; conditional E-value: 7.6e-62 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGa 68 lvi+n+K+++s+ +++ +++ +a +av pf +l + + s + +Aq+v a Ga lcl|FitnessBrowser__Cup4G11:RR42_RS05495 5 LVIGNWKMHGSLAANVTLLEAIKA---APASARLAVCAPFPYLAQCQALLAgSAVAWGAQDVSAEARGA 70 79**********999999999985...6777899**************99999**************** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinn 137 ftGe+ A ml+++Ga + l+gHsErRs++ e+d +++k r+ e g+ +vvCvge+l++rea++t + lcl|FitnessBrowser__Cup4G11:RR42_RS05495 71 FTGEVAASMLAEFGASYALVGHSERRSYHGETDATVAAKAVRALEFGIVPVVCVGESLAQREAGETEAV 139 **************************************************************6666666 PP TIGR00419 138 vattaaaaA.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGa 199 v ++ +a+ l v+A+EPv++iGtGk++s +a++v++++r ++ ++ va + +lyG+ lcl|FitnessBrowser__Cup4G11:RR42_RS05495 140 VGRQLGAVLealsldqLGRIVLAYEPVWAIGTGKTASSEQAQAVHAFLRAQVAARDAGVAARMAMLYGG 208 666666654556666699*************************************************** PP TIGR00419 200 svtaaedaelaaqldvdGvLlasavlkae 228 sv+ ++ael+ +d+dG L+++a+lk++ lcl|FitnessBrowser__Cup4G11:RR42_RS05495 209 SVKPDNAAELFSMPDIDGGLIGGASLKSD 237 ***************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (245 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: 7.72 // [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