Align triosephosphate isomerase subunit (EC 5.3.1.1) (characterized)
to candidate WP_019388787.1 P735_RS0114590 triose-phosphate isomerase
Query= metacyc::MONOMER-13051 (252 letters) >NCBI__GCF_000283015.1:WP_019388787.1 Length = 249 Score = 223 bits (568), Expect = 3e-63 Identities = 114/247 (46%), Positives = 162/247 (65%), Gaps = 1/247 (0%) Query: 3 RTPIIAGNWKLNMNPKETVEFVNAVKDQLPDPSKVESVICAPAVDLDALLKAAEGSNLHV 62 R I+AGNWK+N + +T + A+K Q + E +I A +L + + S + V Sbjct: 2 RKQIVAGNWKMNNDLAQTEALITALKKQTKT-TDAEVMIAPTATNLWQAYNSLKDSKIEV 60 Query: 63 GAENCYWENSGAFTGETSPAVLKEMGVQYVIIGHSERRDYFHETDEDINKKAKAIFANGL 122 A+N ++ +GA+TGE S ++LK +G+ VI+GHSERR+YF+ETDE + KK A A G+ Sbjct: 61 IAQNMHFAENGAYTGEISASMLKSIGINTVILGHSERREYFNETDELLAKKVDAALAKGM 120 Query: 123 TPILCCGESLETREAGKENEWVVSQIKAGLEGLTSEQVSKLVIAYEPIWAIGTGKTASSD 182 I C GE L R+AGKE V +QIK L L + +++AYEP+WAIGTG+TAS + Sbjct: 121 RVIFCFGEELADRKAGKEETVVGNQIKNALFHLNAAAFQNIILAYEPVWAIGTGETASPE 180 Query: 183 QAEEMCKTIRETVKDLYNEETAENVRIQYGGSVKPANVKELMAKPNIDGGLVGGASLVPD 242 QA++M IR+T+ D Y + AE V I YGGSVKPAN +E+ +KP++DGGL+GGASL D Sbjct: 181 QAQDMHAFIRKTLADKYGNDIAEEVSILYGGSVKPANAEEIFSKPDVDGGLIGGASLNAD 240 Query: 243 SYLALVN 249 + A+VN Sbjct: 241 DFFAIVN 247 Lambda K H 0.312 0.130 0.377 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: 178 Number of extensions: 7 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: 252 Length of database: 249 Length adjustment: 24 Effective length of query: 228 Effective length of database: 225 Effective search space: 51300 Effective search space used: 51300 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 (21.8 bits) S2: 46 (22.3 bits)
Align candidate WP_019388787.1 P735_RS0114590 (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.1272623.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-68 216.5 1.1 2.5e-68 216.3 1.1 1.0 1 NCBI__GCF_000283015.1:WP_019388787.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000283015.1:WP_019388787.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 216.3 1.1 2.5e-68 2.5e-68 1 228 [] 5 240 .. 5 240 .. 0.97 Alignments for each domain: == domain 1 score: 216.3 bits; conditional E-value: 2.5e-68 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 +v +n+K+n+ + + e +++ l+++ ++++ ev +ap l + + ++ s+i+v Aqn++ + Ga+tGe NCBI__GCF_000283015.1:WP_019388787.1 5 IVAGNWKMNNDLAQTEALITALKKQT-KTTDAEVMIAPTATNLWQAYNSLKdSKIEVIAQNMHFAENGAYTGE 76 699*******************9985.78899******************99********************* PP TIGR00419 73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartinnv 138 isA mlk +G++ v++gHsErR +++e+del++kkv + ++g++++ C ge l++r+ ++++i+n NCBI__GCF_000283015.1:WP_019388787.1 77 ISASMLKSIGINTVILGHSERREYFNETDELLAKKVDAALAKGMRVIFCFGEELADRKagkeetvVGNQIKNA 149 ********************************************************99888888888999999 PP TIGR00419 139 attaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaaedaela 210 + +aaA+++ ++A+EPv++iGtG ++s+ +a+ +++++r l+ +++ae+v++lyG+sv+ a++ e + NCBI__GCF_000283015.1:WP_019388787.1 150 LFHLNAAAFQNIILAYEPVWAIGTGETASPEQAQDMHAFIRKTLADkYGNDIAEEVSILYGGSVKPANAEEIF 222 99999************************************999977999*********************** PP TIGR00419 211 aqldvdGvLlasavlkae 228 ++dvdG L+++a+l a+ NCBI__GCF_000283015.1:WP_019388787.1 223 SKPDVDGGLIGGASLNAD 240 ***************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (249 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: 12.64 // [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