Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_012506113.1 PAES_RS07805 triose-phosphate isomerase
Query= SwissProt::Q8XKU1 (248 letters) >NCBI__GCF_000020625.1:WP_012506113.1 Length = 252 Score = 241 bits (614), Expect = 1e-68 Identities = 127/248 (51%), Positives = 161/248 (64%), Gaps = 4/248 (1%) Query: 1 MRTPIIAGNWKMHYTIDEAVKLVEELKPLVKD--AKCEVVVCPTFVCLDAVKKAVEGTNI 58 MR I+ GNWKM+ TI EAV+L + + + A CEV + P F L V + GT I Sbjct: 1 MRKKIVVGNWKMNKTIAEAVELSSAIIDQLGEVSASCEVGIAPAFPALSGVHGVISGTGI 60 Query: 59 KVGAQNMHFEEKGAFTGEIAPRMLEAMNIDYVIIGHSERREYFNETDETCNKKVKAAFAH 118 + AQN H+E+ GAFTGE++ RML+ YVI+GHSERR+YF +T+ N KVK A + Sbjct: 61 HLAAQNCHYEDDGAFTGEVSVRMLDEAGCSYVIVGHSERRQYFGDTNPVVNLKVKKALSA 120 Query: 119 NLTPILCCGETLEQRENGTTNDVIKAQITADLEGLTKEQAEKVVIAYEPIWAIGTGKTAT 178 L ILC GETL++RE G T +V+ Q+ LEG+ +VIAYEP+WAIGTGKTA+ Sbjct: 121 GLNVILCVGETLDEREKGITTEVVTCQVKEGLEGVA--DIGDIVIAYEPVWAIGTGKTAS 178 Query: 179 SDQANETIAAIRAMVAEMFGQEVADKVRIQYGGSVKPNTIAEQMAKSDIDGALVGGASLV 238 S QA E A+IRA VA ++ + A VRIQYGGSVKP+ E A DIDG L+GGASL Sbjct: 179 SLQAQEVHASIRATVAGLYSEPAAAGVRIQYGGSVKPSNAEELFAMPDIDGGLIGGASLN 238 Query: 239 AADFAQIV 246 A DF IV Sbjct: 239 AEDFVAIV 246 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: 179 Number of extensions: 11 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: 248 Length of database: 252 Length adjustment: 24 Effective length of query: 224 Effective length of database: 228 Effective search space: 51072 Effective search space used: 51072 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 WP_012506113.1 PAES_RS07805 (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.227699.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-64 204.4 3.5 1.2e-64 204.2 3.5 1.0 1 NCBI__GCF_000020625.1:WP_012506113.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000020625.1:WP_012506113.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 204.2 3.5 1.2e-64 1.2e-64 1 228 [] 5 240 .. 5 240 .. 0.94 Alignments for each domain: == domain 1 score: 204.2 bits; conditional E-value: 1.2e-64 TIGR00419 1 lviinfKlnesvgkvelevaklaeevase.agvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftG 71 +v++n+K+n ++ + ++ + + +++ ++ a +ev++ap f l+ v+ ++ + i++aAqn++ + GaftG NCBI__GCF_000020625.1:WP_012506113.1 5 IVVGNWKMNKTIAEAVELSSAIIDQLGEVsASCEVGIAPAFPALSGVHGVISgTGIHLAAQNCHYEDDGAFTG 77 79************************997257********************999****************** PP TIGR00419 72 eisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvatt... 141 e+s ml ++G+ +v++gHsErR ++ ++ +++ kv ++ gl++++Cvgetl+ere + t ++v+ + NCBI__GCF_000020625.1:WP_012506113.1 78 EVSVRMLDEAGCSYVIVGHSERRQYFGDTNPVVNLKVKKALSAGLNVILCVGETLDEREKGITTEVVTCQvke 150 *************************************************************999999877222 PP TIGR00419 142 ..aaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaaedaelaa 211 +++a + + v+A+EPv++iGtGk++s +a++v++s+r ++ s+ a vr++yG+sv+ +++ el+a NCBI__GCF_000020625.1:WP_012506113.1 151 glEGVADIGDIVIAYEPVWAIGTGKTASSLQAQEVHASIRATVAGlYSEPAAAGVRIQYGGSVKPSNAEELFA 223 22346669********************************99999677778999******************* PP TIGR00419 212 qldvdGvLlasavlkae 228 +d+dG L+++a+l ae NCBI__GCF_000020625.1:WP_012506113.1 224 MPDIDGGLIGGASLNAE 240 **************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (252 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: 17.09 // [ok]
This GapMind analysis is from Sep 24 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