Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_028950432.1 Q385_RS0104030 triose-phosphate isomerase
Query= SwissProt::Q4MQ55 (251 letters) >NCBI__GCF_000619805.1:WP_028950432.1 Length = 250 Score = 213 bits (542), Expect = 3e-60 Identities = 108/243 (44%), Positives = 155/243 (63%), Gaps = 2/243 (0%) Query: 5 IIAGNWKMNKTLSEAVSFVEEVKGQIPAASAVDAVVCSPALFLERLVAATEGTDLQVGAQ 64 ++A NWKMNKT++E++ ++E K + VD ++ L + E T++ +GAQ Sbjct: 4 LVAANWKMNKTVAESIEYIEVFKELVKYVEGVDIMIAPSFTSLSSVSVLIEKTNISLGAQ 63 Query: 65 NMHFEKNGAFTGEISPVALSDLKVGYVVLGHSERREMFAETDESVNKKTIAAFEHGLTPI 124 NM + + GA+TGEISP+ L +L V YV+LGHSERR +F E DE +NKK + A E GL PI Sbjct: 64 NMFYAERGAYTGEISPIMLDELNVKYVILGHSERRHIFGEKDEMINKKVLTAVEFGLRPI 123 Query: 125 VCCGETLEERESGKTFDLVAGQVTKALAGLTEEQVKATVIAYEPIWAIGTGKSSSSADAN 184 +C GETLEERE GKT ++V Q+ +AGL E ++ IAYEP+WAIGTG +++ A Sbjct: 124 LCVGETLEERELGKTMNVVERQIRAGVAGL-EREISLIDIAYEPVWAIGTGVNATVEQAQ 182 Query: 185 EVCAHIRKVVAEAVSPEAAEAVRIQYGGSVKPENIKEYMAQSDIDGALVGGASLEPASFL 244 EV IR ++ + +S + RI YGGSV +N E + D++G LVG ASL+P F Sbjct: 183 EVHHFIRNLIND-ISKGNDKDTRILYGGSVNEKNASELIKAPDVEGFLVGTASLDPQKFY 241 Query: 245 GLL 247 ++ Sbjct: 242 KII 244 Lambda K H 0.313 0.129 0.360 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: 168 Number of extensions: 8 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: 251 Length of database: 250 Length adjustment: 24 Effective length of query: 227 Effective length of database: 226 Effective search space: 51302 Effective search space used: 51302 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: 46 (22.3 bits)
Align candidate WP_028950432.1 Q385_RS0104030 (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.1168604.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-66 208.8 0.5 5.7e-66 208.6 0.5 1.0 1 NCBI__GCF_000619805.1:WP_028950432.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000619805.1:WP_028950432.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 208.6 0.5 5.7e-66 5.7e-66 1 227 [. 4 237 .. 4 238 .. 0.95 Alignments for each domain: == domain 1 score: 208.6 bits; conditional E-value: 5.7e-66 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 lv n+K+n +v + + + +e v ++gv + +ap+f l+ v+ +e ++i+++Aqn+ + Ga+tGe NCBI__GCF_000619805.1:WP_028950432.1 4 LVAANWKMNKTVAESIEYIEVFKELVKYVEGVDIMIAPSFTSLSSVSVLIEkTNISLGAQNMFYAERGAYTGE 76 6999*********************************************99999******************* PP TIGR00419 73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaa. 144 is ml +l +k+v++gHsErR ++ e de+i+kkv ++ e gl++++Cvgetleere ++t+n+v ++ a NCBI__GCF_000619805.1:WP_028950432.1 77 ISPIMLDELNVKYVILGHSERRHIFGEKDEMINKKVLTAVEFGLRPILCVGETLEERELGKTMNVVERQIRAg 149 ******************************************************************9986552 PP TIGR00419 145 aA.....lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaq 212 +A ++ +A+EPv++iGtG+ ++ +a++v++++r+ ++ +sk +++r+lyG+sv+++++ el+ NCBI__GCF_000619805.1:WP_028950432.1 150 VAglereISLIDIAYEPVWAIGTGVNATVEQAQEVHHFIRNLINDISKGNDKDTRILYGGSVNEKNASELIKA 222 3365555445569************************************************************ PP TIGR00419 213 ldvdGvLlasavlka 227 +dv+G+L+++a+l + NCBI__GCF_000619805.1:WP_028950432.1 223 PDVEGFLVGTASLDP 237 ************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (250 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: 16.18 // [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