Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate CA265_RS10795 CA265_RS10795 triose-phosphate isomerase
Query= SwissProt::Q8XKU1 (248 letters) >FitnessBrowser__Pedo557:CA265_RS10795 Length = 253 Score = 219 bits (559), Expect = 3e-62 Identities = 110/249 (44%), Positives = 164/249 (65%), Gaps = 4/249 (1%) Query: 1 MRTPIIAGNWKMHYTIDEAVKLVEELKPLVKDAKCE---VVVCPTFVCLDAVKKAVEGTN 57 MR I+AGNWKM+ +E V L E+ +VKD + ++C F+ L+++ K + G + Sbjct: 1 MRKKIVAGNWKMNLDYNEGVSLFSEIVNMVKDERKGDQLAIICSPFIHLNSLAK-LGGND 59 Query: 58 IKVGAQNMHFEEKGAFTGEIAPRMLEAMNIDYVIIGHSERREYFNETDETCNKKVKAAFA 117 +K+GAQN+ +E GA+TGE + +M++++ +YVI+GHSERR+YF E+D +K K A A Sbjct: 60 VKIGAQNISDKESGAYTGETSAKMVKSVGAEYVILGHSERRQYFAESDALLAEKTKVALA 119 Query: 118 HNLTPILCCGETLEQRENGTTNDVIKAQITADLEGLTKEQAEKVVIAYEPIWAIGTGKTA 177 + LTPI C GETL++R NG+ +V+K Q+ + L + +K+VIAYEP+WAIGTG TA Sbjct: 120 NGLTPIFCIGETLDERNNGSYYEVLKKQLVEGIFSLAEADFKKLVIAYEPVWAIGTGLTA 179 Query: 178 TSDQANETIAAIRAMVAEMFGQEVADKVRIQYGGSVKPNTIAEQMAKSDIDGALVGGASL 237 + QA + A IR+ + +G VAD I YGGS P+ A +++DIDG L+GGASL Sbjct: 180 SPVQAQDIHAFIRSEIQANYGFNVADDTTILYGGSCNPSNAASLFSQNDIDGGLIGGASL 239 Query: 238 VAADFAQIV 246 + DF I+ Sbjct: 240 KSRDFTDII 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: 174 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: 248 Length of database: 253 Length adjustment: 24 Effective length of query: 224 Effective length of database: 229 Effective search space: 51296 Effective search space used: 51296 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 CA265_RS10795 CA265_RS10795 (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.20446.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.9e-63 198.0 0.0 1.2e-62 197.8 0.0 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS10795 CA265_RS10795 triose-phosphate i Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS10795 CA265_RS10795 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 197.8 0.0 1.2e-62 1.2e-62 1 227 [. 5 241 .. 5 242 .. 0.89 Alignments for each domain: == domain 1 score: 197.8 bits; conditional E-value: 1.2e-62 TIGR00419 1 lviinfKlnesvgkvelevaklaeevase.agveva.vappfvdldvvkdeveseiqvaAqnvdavks 66 +v +n+K+n ++ + +++ + v +e +g ++a + pf++l+ +++ ++++++Aqn+ ++s lcl|FitnessBrowser__Pedo557:CA265_RS10795 5 IVAGNWKMNLDYNEGVSLFSEIVNMVKDErKGDQLAiICSPFIHLNSLAKLGGNDVKIGAQNISDKES 72 6999***7777777777777777766654144555526889*******999999************** PP TIGR00419 67 GaftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaart 134 Ga+tGe+sA+m+k +Ga++v++gHsErR +++e+d l+++k ++ + gl+++ C+getl+er+ ++ lcl|FitnessBrowser__Pedo557:CA265_RS10795 73 GAYTGETSAKMVKSVGAEYVILGHSERRQYFAESDALLAEKTKVALANGLTPIFCIGETLDERNNGSY 140 ******************************************************************99 PP TIGR00419 135 innvattaaaaA.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvr 194 ++++++ +++ v+A+EPv++iGtG ++s+ +a+ +++++r ++ +va+++ lcl|FitnessBrowser__Pedo557:CA265_RS10795 141 YEVLKKQLVEGIfslaeadFKKLVIAYEPVWAIGTGLTASPVQAQDIHAFIRSEIQAnYGFNVADDTT 208 9998887532222344667**********************************99987899******* PP TIGR00419 195 vlyGasvtaaedaelaaqldvdGvLlasavlka 227 +lyG+s + +++a l+ q d+dG L+++a+lk+ lcl|FitnessBrowser__Pedo557:CA265_RS10795 209 ILYGGSCNPSNAASLFSQNDIDGGLIGGASLKS 241 *******************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (253 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: 8.38 // [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