Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_078716775.1 B5D49_RS06130 triose-phosphate isomerase
Query= BRENDA::A8B3A8 (249 letters) >NCBI__GCF_900167125.1:WP_078716775.1 Length = 251 Score = 181 bits (458), Expect = 2e-50 Identities = 107/248 (43%), Positives = 140/248 (56%), Gaps = 10/248 (4%) Query: 8 VGGNWKMHGSKNSIRDICNTLKG---ASLDPNVEVIVACPAPYLDYCRSLLP--PSVALA 62 + NWKM+ + N RD + L L N EV++ P L L P +A Sbjct: 5 MAANWKMYKTWNQARDTASELAQNIRGQLPENREVLIFPPFTALKGVAEALQNEPGMAAG 64 Query: 63 AQNCYKVEQGAFTGEISPGMIKDCGGQWVILGHSERRHVFKEDDVLIGEKIKHALESGLN 122 AQN Y +GAFTGEISP M+ D G WV+ GHSERRHV ED+ +G K AL + LN Sbjct: 65 AQNMYPAAEGAFTGEISPDMLLDVGASWVLTGHSERRHVLGEDNAFVGRKTAFALNNNLN 124 Query: 123 VIACIGELLEDREAGRTEEVCFRQIKHIASNVK---DWSKVVIAYEPVWAIGTGKTATPD 179 VI CIGEL+E+R A R EEV Q++ + + +VIAYEPVWAIGTG+ A PD Sbjct: 125 VILCIGELIEERRADRVEEVLSEQLEAGLAEIPVGLTSDSLVIAYEPVWAIGTGEVAGPD 184 Query: 180 QAQEVHSKVRNWLSTNVSADVASKVRIQYGGSVNAGNCKELGRKPDIDGFLVGGASLKPE 239 + H+ VR + + +AS++ I YGGSV N + ++DG LVGGASL E Sbjct: 185 EIATTHTFVRKKIE-ELLPSIASEISILYGGSVKPDNISAIMTLDNVDGVLVGGASLTAE 243 Query: 240 -FVQIINA 246 F +I+ A Sbjct: 244 SFSKIVLA 251 Lambda K H 0.318 0.135 0.418 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: 193 Number of extensions: 9 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: 249 Length of database: 251 Length adjustment: 24 Effective length of query: 225 Effective length of database: 227 Effective search space: 51075 Effective search space used: 51075 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 bits)
Align candidate WP_078716775.1 B5D49_RS06130 (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.2551866.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-52 164.6 0.0 1.8e-52 164.4 0.0 1.0 1 NCBI__GCF_900167125.1:WP_078716775.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900167125.1:WP_078716775.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 164.4 0.0 1.8e-52 1.8e-52 2 228 .] 5 243 .. 4 243 .. 0.92 Alignments for each domain: == domain 1 score: 164.4 bits; conditional E-value: 1.8e-52 TIGR00419 2 viinfKlnesvgkvelevaklaeevase..agvevavappfvdldvvkdeve..seiqvaAqnvdavksGaft 70 + n+K+ + ++ ++la+++ ++ ++ ev + ppf l+ v+++++ + + +Aqn+ Gaft NCBI__GCF_900167125.1:WP_078716775.1 5 MAANWKMYKTWNQARDTASELAQNIRGQlpENREVLIFPPFTALKGVAEALQnePGMAAGAQNMYPAAEGAFT 77 578***9999999999999999999886226789****************9866779999************* PP TIGR00419 71 GeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaa 143 Geis +ml d+Ga +vl gHsErR +l e + +++ k a + + +l++++C+ge eer a r +++ ++ + NCBI__GCF_900167125.1:WP_078716775.1 78 GEISPDMLLDVGASWVLTGHSERRHVLGEDNAFVGRKTAFALNNNLNVILCIGELIEERRADRVEEVLSEQLE 150 ************************************************************9998888888866 PP TIGR00419 144 aaA........lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedae 208 a ++ v+A+EPv++iGtG ++ + e + +vr +++ + +a ++++lyG+sv+ + NCBI__GCF_900167125.1:WP_078716775.1 151 AGLaeipvgltSDSLVIAYEPVWAIGTGEVAGPDEIATTHTFVRKKIEELLPSIASEISILYGGSVKPDNISA 223 6434899995555669***************************************************999999 PP TIGR00419 209 laaqldvdGvLlasavlkae 228 + +vdGvL+++a+l ae NCBI__GCF_900167125.1:WP_078716775.1 224 IMTLDNVDGVLVGGASLTAE 243 888889***********986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (251 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: 13.82 // [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