Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_011320017.1 AVA_RS16660 triose-phosphate isomerase
Query= BRENDA::P00943 (253 letters) >NCBI__GCF_000204075.1:WP_011320017.1 Length = 241 Score = 226 bits (576), Expect = 3e-64 Identities = 125/250 (50%), Positives = 172/250 (68%), Gaps = 15/250 (6%) Query: 1 MRKPIIAGNWKMHKTLAEAVQFVED---VKGHVPPADEVISVVCAPFLFLDRLVQAADGT 57 MRK +IAGNWKM KT AE+ +F+++ P EV+ +C PF L L Q+ G+ Sbjct: 1 MRKIVIAGNWKMFKTQAESQEFLKEFLPALEETPQEREVL--LCVPFTDLAILSQSLHGS 58 Query: 58 DLKIGAQTMHFADQGAYTGEVSPVMLKDLGVTYVILGHSERRQMFAETDETVNKKVLAAF 117 +++GAQ +H+A+ GAYTGE+S ML ++GV YVI+GHSERRQ F ETDETVN ++ AA Sbjct: 59 LVQLGAQNVHWAENGAYTGEISGPMLTEIGVRYVIVGHSERRQFFGETDETVNLRLQAAQ 118 Query: 118 TRGLIPIICCGESLEEREAGQTNAVVASQVEKALAGLTPEQVKQAVIAYEPIWAIGTGKS 177 GL PI+C GE+ ++R++G+T +++ SQ++K L + + VIAYEPIWAIGTG + Sbjct: 119 KYGLTPILCVGETKQQRDSGETESLIVSQLDKDLINVDQTNL---VIAYEPIWAIGTGDT 175 Query: 178 STPEDANSVCGHIRSVVSRLFGPEAAEAIRIQYGGSVKPDNIRDFLAQQQIDGPLVGGAS 237 +AN V G IR S+L P+ + IQYGGSVKP+NI + +AQ +IDG LVGGAS Sbjct: 176 CETTEANRVIGLIR---SQLKNPD----VPIQYGGSVKPNNIDEIMAQPEIDGVLVGGAS 228 Query: 238 LEPASFLQLV 247 LE ASF ++V Sbjct: 229 LEAASFARIV 238 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: 190 Number of extensions: 12 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: 241 Length adjustment: 24 Effective length of query: 229 Effective length of database: 217 Effective search space: 49693 Effective search space used: 49693 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_011320017.1 AVA_RS16660 (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.24547.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-54 169.6 0.0 5.6e-54 169.4 0.0 1.0 1 lcl|NCBI__GCF_000204075.1:WP_011320017.1 AVA_RS16660 triose-phosphate iso Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000204075.1:WP_011320017.1 AVA_RS16660 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 169.4 0.0 5.6e-54 5.6e-54 1 227 [. 5 231 .. 5 232 .. 0.92 Alignments for each domain: == domain 1 score: 169.4 bits; conditional E-value: 5.6e-54 TIGR00419 1 lviinfKlnesvgkvelevaklaeevas.eagvevavappfvdldvvkdeve.seiqvaAqnvdavksG 67 ++ +n+K+ + + ++ + + + + +++ ev + +pf dl ++++ ++ s +q++Aqnv+ + G lcl|NCBI__GCF_000204075.1:WP_011320017.1 5 VIAGNWKMFKTQAESQEFLKEFLPALEEtPQEREVLLCVPFTDLAILSQSLHgSLVQLGAQNVHWAENG 73 5889***999999999999999998877257789******************999************** PP TIGR00419 68 aftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartin 136 a+tGeis ml ++G+++v++gHsErR ++ e+de ++ ++ +++ gl++++Cvget+++r++++t lcl|NCBI__GCF_000204075.1:WP_011320017.1 74 AYTGEISGPMLTEIGVRYVIVGHSERRQFFGETDETVNLRLQAAQKYGLTPILCVGETKQQRDSGETES 142 ***************************************************************999877 PP TIGR00419 137 nvatt..aaaaA..lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasv 201 + + + + ++ v+A+EP+++iGtG + ea+ v + +r s+ +++v ++yG+sv lcl|NCBI__GCF_000204075.1:WP_011320017.1 143 LIVSQldKDLINvdQTNLVIAYEPIWAIGTGDTCETTEANRVIGLIR------SQLKNPDVPIQYGGSV 205 776652123333448999*****************************......555699********** PP TIGR00419 202 taaedaelaaqldvdGvLlasavlka 227 + ++ e +aq+++dGvL+++a+l a lcl|NCBI__GCF_000204075.1:WP_011320017.1 206 KPNNIDEIMAQPEIDGVLVGGASLEA 231 ***********************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (241 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: 10.34 // [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