Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_014448271.1 LFE_RS00225 triose-phosphate isomerase
Query= BRENDA::Q5S7Y5 (282 letters) >NCBI__GCF_000284315.1:WP_014448271.1 Length = 265 Score = 145 bits (367), Expect = 7e-40 Identities = 89/241 (36%), Positives = 133/241 (55%), Gaps = 21/241 (8%) Query: 38 NWKCNGSVANVAKLVDELNAGTI-----PRGVDVVVAPPFIYIDYVMQHLDRDK---YQL 89 NWK N + A + +D L+A I G+++ +AP +Y+D++++ + R+K ++ Sbjct: 6 NWKMNMTRAQINDYLDVLSASPIWPALEEAGIEIALAPSSVYLDHLVRSI-REKELPIRV 64 Query: 90 SAQNAWIGGNGAFTGEVSAEQLTDFGVPWVILGHSERRSLFGESNEVVAKKTSHALAAGL 149 AQ+ +GAFTGE+ L D GV VILGHSERR FGE++E V KT L AGL Sbjct: 65 VAQDVSTRTSGAFTGEIGVPNLLDIGVSGVILGHSERRRFFGETDEDVCDKTDLCLRAGL 124 Query: 150 GVIACIGETLEQRNSGSVFKVLDAQMDALVD------EVKDWTKVVLAYEPVWAIGTGVV 203 I C GE+ R SG F V+ Q+ + D E +T + LAYEP+WAIG+G+V Sbjct: 125 MPIICFGESSADRKSGRAFDVIKTQLQPVADRANLLREDGVYTALFLAYEPIWAIGSGIV 184 Query: 204 ASPEQAQEVHAYLRQYCAKKLGAAVADKLRIIYGGSVSDTNCKDLSKQEDIDGFLVGGAS 263 A EV A+ G ++ + +YGGS++ N ++S + + GFLVG + Sbjct: 185 AGATDVCEVTAFGFD------GFTWPERPKFLYGGSITSDNIVEISACDKLSGFLVGSSW 238 Query: 264 L 264 L Sbjct: 239 L 239 Lambda K H 0.318 0.132 0.392 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: 196 Number of extensions: 11 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: 282 Length of database: 265 Length adjustment: 25 Effective length of query: 257 Effective length of database: 240 Effective search space: 61680 Effective search space used: 61680 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: 47 (22.7 bits)
Align candidate WP_014448271.1 LFE_RS00225 (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.1713981.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-46 143.2 0.0 8.8e-46 142.5 0.0 1.3 1 NCBI__GCF_000284315.1:WP_014448271.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000284315.1:WP_014448271.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 142.5 0.0 8.8e-46 8.8e-46 1 227 [. 2 241 .. 2 242 .. 0.93 Alignments for each domain: == domain 1 score: 142.5 bits; conditional E-value: 8.8e-46 TIGR00419 1 lviinfKlnesvgkvelevaklae.ev...aseagvevavappfvdldvvkdeve.se..iqvaAqnvdavks 66 l++ n+K+n ++ + + + l++ + +eag+e+a+ap+ v+ld +++ ++ e i+v+Aq+v + +s NCBI__GCF_000284315.1:WP_014448271.1 2 LLVANWKMNMTRAQINDYLDVLSAsPIwpaLEEAGIEIALAPSSVYLDHLVRSIReKElpIRVVAQDVSTRTS 74 5789****************9998544332699******************99985335599*********** PP TIGR00419 67 GaftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnva 139 GaftGei l d+G+ gv++gHsErR ++ e+de + k + gl++++C ge+ ++r+++r +++++ NCBI__GCF_000284315.1:WP_014448271.1 75 GAFTGEIGVPNLLDIGVSGVILGHSERRRFFGETDEDVCDKTDLCLRAGLMPIICFGESSADRKSGRAFDVIK 147 ************************************************************************* PP TIGR00419 140 ttaaaaA...........lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasv 201 t+ + +A ++ ++A+EP+++iG+G+++ + +v+++ d + e + lyG+s+ NCBI__GCF_000284315.1:WP_014448271.1 148 TQLQPVAdranllredgvYTALFLAYEPIWAIGSGIVAGATDVCEVTAFGFDGF-----TWPERPKFLYGGSI 215 ****9999***************************************9987544.....4568899******* PP TIGR00419 202 taaedaelaaqldvdGvLlasavlka 227 t+ + +e a G+L++s+ l + NCBI__GCF_000284315.1:WP_014448271.1 216 TSDNIVEISACDKLSGFLVGSSWLDP 241 *********************98765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (265 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: 9.54 // [ok]
This GapMind analysis is from Apr 09 2024. 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