Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate 207136 DVU1677 triosephosphate isomerase
Query= SwissProt::P00943 (253 letters) >MicrobesOnline__882:207136 Length = 251 Score = 194 bits (493), Expect = 1e-54 Identities = 113/253 (44%), Positives = 154/253 (60%), Gaps = 9/253 (3%) Query: 3 KPIIAGNWKMHKTLAEAV----QFVEDVKGHVPPADEVISVVCAPFLFLDRLVQA-ADGT 57 K +IA NWKM+KT+ EA + V V G +P EV+ VC PF L L D Sbjct: 2 KKLIAANWKMYKTIDEARATGRELVSAVAGSLPADREVL--VCPPFTALHALHDTFKDVE 59 Query: 58 DLKIGAQTMHFADQGAYTGEVSPVMLKDLGVTYVILGHSERRQMFAETDETVNKKVLAAF 117 IG Q ++ A +GAYTGE++P ML D G +V+ GHSERR + E DETV +K + Sbjct: 60 GFAIGGQDVYPATEGAYTGEIAPGMLLDAGCGWVLTGHSERRHILGEDDETVARKTAFSL 119 Query: 118 TRGLIPIICCGESLEEREAGQTNAVVASQVEKALAGLTPEQVKQA-VIAYEPIWAIGTGK 176 GL ++C GE L+EREAG+ V+A Q++ LA + V Q+ V+AYEP+WAIGTGK Sbjct: 120 KAGLRVVLCIGEKLDEREAGRLEDVLAHQLQVGLADVDATYVPQSLVVAYEPVWAIGTGK 179 Query: 177 SSTPEDANSVCGHIRSVVSRLFGPEAAEAIRIQYGGSVKPDNIRDFLAQQQIDGPLVGGA 236 + P + +RS++ +G + A AIRI YGGSVKPDN + L+ +DG LVGGA Sbjct: 180 VAGPAEVVEAHALVRSLLEARYGRDGA-AIRILYGGSVKPDNAAELLSLDNVDGLLVGGA 238 Query: 237 SLEPASFLQLVEA 249 SL+ SF +++ A Sbjct: 239 SLQAVSFSRIILA 251 Lambda K H 0.318 0.134 0.389 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: 197 Number of extensions: 10 Number of successful extensions: 4 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: 253 Length of database: 251 Length adjustment: 24 Effective length of query: 229 Effective length of database: 227 Effective search space: 51983 Effective search space used: 51983 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 (21.7 bits) S2: 46 (22.3 bits)
Align candidate 207136 DVU1677 (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.13100.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-50 156.5 0.0 5.5e-50 156.3 0.0 1.0 1 lcl|MicrobesOnline__882:207136 DVU1677 triosephosphate isomeras Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:207136 DVU1677 triosephosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 156.3 0.0 5.5e-50 5.5e-50 1 227 [. 4 242 .. 4 243 .. 0.91 Alignments for each domain: == domain 1 score: 156.3 bits; conditional E-value: 5.5e-50 TIGR00419 1 lviinfKlnesvgkvelevaklaeevas..eagvevavappfvdldvvkdeve..seiqvaAqnvdavksGaftGeisA 75 l+ n+K+ ++ + +l va+ +a+ ev v ppf l+ ++d + ++ q+v + Ga+tGei lcl|MicrobesOnline__882:207136 4 LIAANWKMYKTIDEARATGRELVSAVAGslPADREVLVCPPFTALHALHDTFKdvEGFAIGGQDVYPATEGAYTGEIAP 82 6889***988999988888888888887335899***************998854578999****************** PP TIGR00419 76 emlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaa.aA....... 146 ml d+G+ +vl gHsErR +l e de ++ k a + gl++v+C+ge l+erea+r +++a++ ++ A lcl|MicrobesOnline__882:207136 83 GMLLDAGCGWVLTGHSERRHILGEDDETVARKTAFSLKAGLRVVLCIGEKLDEREAGRLEDVLAHQLQVgLAdvdatyv 161 *********************************************************9999998886652346777755 PP TIGR00419 147 lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvdGvLlasavl 225 ++ vvA+EPv++iGtGk++ +Ae + ++ vr l+ +r+lyG+sv+ ++ael +vdG+L+++a+l lcl|MicrobesOnline__882:207136 162 PQSLVVAYEPVWAIGTGKVAGPAEVVEAHALVRSLLEARYGRDGAAIRILYGGSVKPDNAAELLSLDNVDGLLVGGASL 240 56779****************************9999988888999******************999***********9 PP TIGR00419 226 ka 227 +a lcl|MicrobesOnline__882:207136 241 QA 242 87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (251 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: 8.77 // [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