Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_034632744.1 G496_RS0107365 triose-phosphate isomerase
Query= BRENDA::A2FT29 (252 letters) >NCBI__GCF_000429985.1:WP_034632744.1 Length = 247 Score = 184 bits (467), Expect = 1e-51 Identities = 106/240 (44%), Positives = 147/240 (61%), Gaps = 10/240 (4%) Query: 6 VGGNWKANPKTVQEAEKLVEMLNGAKVEGNV----EVVVAAPFVFLPTLQQKL-RKDW-K 59 + NWK KT EAEK + L +K+EG V EV++AAPF L ++ L +DW Sbjct: 1 MAANWKMF-KTRSEAEKTAQTLL-SKIEGKVPADREVLIAAPFTALSSVDSVLGSQDWFH 58 Query: 60 VSAENVFTKPNGAFTGEVTVPMIKSFGIEWTILGHSERRDILKEDDEFLAAKAKFALENG 119 +S EN++ GAFTGE++ M+K G + + GHSERR I+ E DEF+ K F L N Sbjct: 59 LSGENMYPAKEGAFTGEISADMLKDCGCGFCLAGHSERRHIMGESDEFVGEKVTFGLAND 118 Query: 120 MKIIYCCGEHLSEREAGKASEFVSAQIEKMIPAIPAGKWDD-VVIAYEPIWAIGTGKVAS 178 + +I C GE + ER+AG + + Q+EK + + A D +VIAYEP+WAIGTG+VA Sbjct: 119 LSMILCVGETIEERKAGNVQQVIDTQLEKGLAGVEADIVPDRIVIAYEPVWAIGTGEVAG 178 Query: 179 TQDAQEMCKVIRDILAAKVGADIANKVRILYGGSVKPNNCNELAACPDVDGFLVGGASLE 238 ++ +E +R L + D N ++ILYGGSVKP NC E+ A +VDG LVGGASL+ Sbjct: 179 PEEIKEAHLFVRKKL-ENIFPDKFNDIKILYGGSVKPGNCAEIIALDNVDGVLVGGASLD 237 Lambda K H 0.318 0.134 0.400 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: 194 Number of extensions: 7 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: 252 Length of database: 247 Length adjustment: 24 Effective length of query: 228 Effective length of database: 223 Effective search space: 50844 Effective search space used: 50844 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 WP_034632744.1 G496_RS0107365 (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.aa/TIGR00419.hmm # target sequence database: /tmp/gapView.26720.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-54 170.1 0.0 3.7e-54 169.9 0.0 1.0 1 lcl|NCBI__GCF_000429985.1:WP_034632744.1 G496_RS0107365 triose-phosphate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429985.1:WP_034632744.1 G496_RS0107365 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 169.9 0.0 3.7e-54 3.7e-54 4 226 .. 3 237 .. 1 239 [. 0.89 Alignments for each domain: == domain 1 score: 169.9 bits; conditional E-value: 3.7e-54 TIGR00419 4 infKlnesvgkvelevaklaeevas..eagvevavappfvdldvvkdevese..iqvaAqnvdavksGa 68 n+K+ ++++ e+ ++l ++ + +a+ ev +a pf l+ v + s+ ++ n+ k Ga lcl|NCBI__GCF_000429985.1:WP_034632744.1 3 ANWKMFKTRSEAEKTAQTLLSKIEGkvPADREVLIAAPFTALSSVDSVLGSQdwFHLSGENMYPAKEGA 71 79**9999998888877777777662257899*************99998543489************* PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinn 137 ftGeisA+mlkd+G+ + l gHsErR ++ e+de++++kv+ + +l ++Cvget eer+a++ ++ lcl|NCBI__GCF_000429985.1:WP_034632744.1 72 FTGEISADMLKDCGCGFCLAGHSERRHIMGESDEFVGEKVTFGLANDLSMILCVGETIEERKAGNVQQV 140 ***************************************************************999888 PP TIGR00419 138 vatt.aaaaA.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyG 198 + t+ ++ A + v+A+EPv++iGtG ++ + e ++ + +vr l+++ ++ +++++lyG lcl|NCBI__GCF_000429985.1:WP_034632744.1 141 IDTQlEKGLAgveadivPDRIVIAYEPVWAIGTGEVAGPEEIKEAHLFVRKKLENIFPDKFNDIKILYG 209 88874344445666754556699********************************************** PP TIGR00419 199 asvtaaedaelaaqldvdGvLlasavlk 226 +sv+ +++ae +a +vdGvL+++a+l lcl|NCBI__GCF_000429985.1:WP_034632744.1 210 GSVKPGNCAEIIALDNVDGVLVGGASLD 237 *************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (247 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 6.05 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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