Align triosephosphate isomerase subunit (EC 5.3.1.1) (characterized)
to candidate WP_092052981.1 BQ4888_RS02030 triose-phosphate isomerase
Query= metacyc::MONOMER-13055 (252 letters) >NCBI__GCF_900111775.1:WP_092052981.1 Length = 255 Score = 237 bits (604), Expect = 2e-67 Identities = 121/246 (49%), Positives = 166/246 (67%) Query: 3 RKPIIAGNWKMNKTLSEAQAFVEAVKNNLPSSDNVESVIGAPALFLAPMAYLRQGSELKL 62 RKP+IAGNWK++KT+ EA A+K D+++ VI LA +A GS + L Sbjct: 2 RKPMIAGNWKLHKTIGEALDLASALKQETAEIDDIDIVIAPVFTSLAKVAEQLVGSNIAL 61 Query: 63 AAENSYFENAGAFTGENSPAAIVDLGVEYIIIGHSERREYFHETDEDINKKAKAIFAAGA 122 A +N + +GAFTGE SPA + D G Y I+GHSERR+ F ETD IN+K +++ AAG Sbjct: 62 AGQNCHPAASGAFTGEVSPALLRDAGCRYCIVGHSERRQLFGETDAFINEKVRSLLAAGL 121 Query: 123 TPILCCGETLETFEAGKTAEWVSGQIEAGLAGLSAEQVSNLVIAYEPIWAIGTGKTATNE 182 I C GETLE E + E ++ Q+ GL ++A Q+S +V+AYEP+WAIGTGKTA+N Sbjct: 122 DVIFCIGETLEEREGDQMYEVLATQVREGLRDITAAQMSQVVVAYEPVWAIGTGKTASNL 181 Query: 183 IADETCGVVRSTVEKLYGKEVSEAVRIQYGGSVKPETIEGLMAKENIDGALVGGASLEAD 242 A+E VR + LY +EV+E+ RI YGGSVKP+ ++GLMA+ ++DGALVGGASL+AD Sbjct: 182 QAEEAHAFVRGLLRGLYSEEVAESTRILYGGSVKPDNVDGLMAQMDVDGALVGGASLKAD 241 Query: 243 SFLALL 248 FL ++ Sbjct: 242 DFLRII 247 Lambda K H 0.312 0.130 0.365 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: 191 Number of extensions: 5 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: 252 Length of database: 255 Length adjustment: 24 Effective length of query: 228 Effective length of database: 231 Effective search space: 52668 Effective search space used: 52668 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 47 (22.7 bits)
Align candidate WP_092052981.1 BQ4888_RS02030 (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.15694.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.1e-70 221.6 0.3 7e-70 221.4 0.3 1.0 1 lcl|NCBI__GCF_900111775.1:WP_092052981.1 BQ4888_RS02030 triose-phosphate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900111775.1:WP_092052981.1 BQ4888_RS02030 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 221.4 0.3 7e-70 7e-70 1 228 [] 5 241 .. 5 241 .. 0.94 Alignments for each domain: == domain 1 score: 221.4 bits; conditional E-value: 7e-70 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGa 68 ++ +n+Kl+ ++g+ + + l++e a+ +++ +++ap f l v++++ s+i +a qn++ sGa lcl|NCBI__GCF_900111775.1:WP_092052981.1 5 MIAGNWKLHKTIGEALDLASALKQETAEIDDIDIVIAPVFTSLAKVAEQLVgSNIALAGQNCHPAASGA 73 5899********************************************9888***************** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere....... 130 ftGe+s ++l+d+G+++ ++gHsErR l+ e+d +i++kv l + gl ++ C+getleere lcl|NCBI__GCF_900111775.1:WP_092052981.1 74 FTGEVSPALLRDAGCRYCIVGHSERRQLFGETDAFINEKVRSLLAAGLDVIFCIGETLEEREgdqmyev 142 **************************************************************5555555 PP TIGR00419 131 aartinnvattaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyG 198 a+++ ++ +aa ++++vvA+EPv++iGtGk++s+ +ae+ +++vr l+ s+evaes+r+lyG lcl|NCBI__GCF_900111775.1:WP_092052981.1 143 LATQVREGLRDITAAQMSQVVVAYEPVWAIGTGKTASNLQAEEAHAFVRGLLRGlYSEEVAESTRILYG 211 4445555555566777***********************************999899************ PP TIGR00419 199 asvtaaedaelaaqldvdGvLlasavlkae 228 +sv+ + l+aq+dvdG+L+++a+lka+ lcl|NCBI__GCF_900111775.1:WP_092052981.1 212 GSVKPDNVDGLMAQMDVDGALVGGASLKAD 241 ****************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (255 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: 10.48 // [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