Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_058858668.1 AS188_RS09635 triose-phosphate isomerase
Query= BRENDA::P9WG43 (261 letters) >NCBI__GCF_001482365.1:WP_058858668.1 Length = 271 Score = 324 bits (830), Expect = 1e-93 Identities = 162/252 (64%), Positives = 196/252 (77%), Gaps = 2/252 (0%) Query: 3 RKPLIAGNWKMNLNHYEAIALVQKIAFSLPDKYYD--RVDVAVIPPFTDLRSVQTLVDGD 60 R PLIAGNWKMN++H + IAL+QK+A++L D +D RV+VAV PPFTDLRSVQ+LV+ D Sbjct: 11 RTPLIAGNWKMNMDHVQGIALLQKLAWTLDDAKHDHDRVEVAVFPPFTDLRSVQSLVEAD 70 Query: 61 KLRLTYGAQDLSPHDSGAYTGDVSGAFLAKLGCSYVVVGHSERRTYHNEDDALVAAKAAT 120 LR+ YGAQDLS DSGAYTGDVSG FLA+LGC+YV+VGHSERRT H E DAL AAK A Sbjct: 71 GLRVRYGAQDLSDKDSGAYTGDVSGQFLARLGCTYVLVGHSERRTLHGETDALCAAKIAA 130 Query: 121 ALKHGLTPIVCIGEHLDVREAGNHVAHNIEQLRGSLAGLLAEQIGSVVIAYEPVWAIGTG 180 A +HGL P++C+GE L+VR+AG HV H +EQLRG++AGL AE++ +V+AYEPVWAIGTG Sbjct: 131 AHRHGLVPVLCVGEGLEVRQAGEHVGHTLEQLRGAVAGLDAERVAELVVAYEPVWAIGTG 190 Query: 181 RVASAADAQEVCAAIRKELASLASPRIADTVRVLYGGSVNAKNVGDIVAQDDVDGGLVGG 240 VA DAQE+ AAIR ELA L R A R+LYGGS A N ++ DVDG LVGG Sbjct: 191 EVAGPEDAQEMAAAIRAELADLHDARTAARTRILYGGSAKAANAAALLKGRDVDGLLVGG 250 Query: 241 ASLDGEHFATLA 252 ASLD E FA++A Sbjct: 251 ASLDAEEFASIA 262 Lambda K H 0.318 0.135 0.393 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: 242 Number of extensions: 8 Number of successful extensions: 2 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: 261 Length of database: 271 Length adjustment: 25 Effective length of query: 236 Effective length of database: 246 Effective search space: 58056 Effective search space used: 58056 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_058858668.1 AS188_RS09635 (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.2009082.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-55 173.0 0.1 4.9e-55 172.8 0.1 1.0 1 NCBI__GCF_001482365.1:WP_058858668.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001482365.1:WP_058858668.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 172.8 0.1 4.9e-55 4.9e-55 1 228 [] 14 256 .. 14 256 .. 0.91 Alignments for each domain: == domain 1 score: 172.8 bits; conditional E-value: 4.9e-55 TIGR00419 1 lviinfKlnesvgkvelevaklaeev....aseagvevavappfvdldvvkdeve...seiqvaAqnvdavks 66 l+ +n+K+n + +++kla + +++ vevav ppf dl+ v+ ve +++ +Aq++ ++s NCBI__GCF_001482365.1:WP_058858668.1 14 LIAGNWKMNMDHVQGIALLQKLAWTLddakHDHDRVEVAVFPPFTDLRSVQSLVEadgLRVRYGAQDLSDKDS 86 6899***9999999888999988766221145678*****************999523357789********* PP TIGR00419 67 GaftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnva 139 Ga+tG++s + l+ lG+ +vl+gHsErR+l+ e+d l ++k+a ++ gl +v+Cvge le r+a++++ + NCBI__GCF_001482365.1:WP_058858668.1 87 GAYTGDVSGQFLARLGCTYVLVGHSERRTLHGETDALCAAKIAAAHRHGLVPVLCVGEGLEVRQAGEHVGHTL 159 ******************************************************************9998777 PP TIGR00419 140 tt.aaaaA......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaa 204 ++ ++a+A + vvA+EPv++iGtG ++ + +a+++ + +r l+ ++ a +r+lyG+s +aa NCBI__GCF_001482365.1:WP_058858668.1 160 EQlRGAVAgldaerVAELVVAYEPVWAIGTGEVAGPEDAQEMAAAIRAELADlHDARTAARTRILYGGSAKAA 232 663677789999999999*********************************9899****************** PP TIGR00419 205 edaelaaqldvdGvLlasavlkae 228 ++a l dvdG+L+++a+l ae NCBI__GCF_001482365.1:WP_058858668.1 233 NAAALLKGRDVDGLLVGGASLDAE 256 *********************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (271 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: 13.51 // [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