Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_028485431.1 A377_RS0109085 triose-phosphate isomerase
Query= BRENDA::P0A858 (255 letters) >NCBI__GCF_000384235.1:WP_028485431.1 Length = 255 Score = 256 bits (654), Expect = 3e-73 Identities = 135/255 (52%), Positives = 172/255 (67%), Gaps = 4/255 (1%) Query: 1 MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDM---AKREAEGS 57 MR V GNWK++GS+ V L++ L K+ +A+ PP +YID A R A Sbjct: 1 MRQKFVAGNWKMHGSKASVEALMAGLIKQADQAGAAKIAVCPPSLYIDQVVTALRNAGCE 60 Query: 58 HIMLGAQNVDLNL-SGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVL 116 +I +GAQN+ SGAFTGE SA MLKD+G +++I+GHSERR E++E++A+K Sbjct: 61 NIAVGAQNMTTEPDSGAFTGEVSARMLKDVGCEFVILGHSERRAMFAETNEVVAEKVKTA 120 Query: 117 KEQGLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGK 176 E LTP+LCIGET AE EAGK E V + Q++AVL G AF VIAYEPVWAIGTGK Sbjct: 121 LENDLTPILCIGETLAEREAGKLEAVISEQVEAVLSVVGIDAFAKIVIAYEPVWAIGTGK 180 Query: 177 SATPAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGAS 236 +A+ QAQ VH FIR +AK + +AE+V+IQYGGS+ NA EL AQPDIDG L+GGAS Sbjct: 181 TASADQAQEVHAFIRGQLAKSNPQVAEKVVIQYGGSMKPVNAQELMAQPDIDGGLIGGAS 240 Query: 237 LKADAFAVIVKAAEA 251 LKA+ F I +AA A Sbjct: 241 LKAEDFIAICQAAGA 255 Lambda K H 0.316 0.130 0.366 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: 177 Number of extensions: 5 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: 255 Length of database: 255 Length adjustment: 24 Effective length of query: 231 Effective length of database: 231 Effective search space: 53361 Effective search space used: 53361 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 (21.6 bits) S2: 47 (22.7 bits)
Align candidate WP_028485431.1 A377_RS0109085 (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.9515.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-73 232.0 6.1 4.5e-73 231.8 6.1 1.0 1 lcl|NCBI__GCF_000384235.1:WP_028485431.1 A377_RS0109085 triose-phosphate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384235.1:WP_028485431.1 A377_RS0109085 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 231.8 6.1 4.5e-73 4.5e-73 1 228 [] 5 244 .. 5 244 .. 0.95 Alignments for each domain: == domain 1 score: 231.8 bits; conditional E-value: 4.5e-73 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve....seiqvaAqnvdav. 64 +v +n+K+++s +ve ++a l ++ + ++av pp +++d v+ +++ +i v+Aqn+ + lcl|NCBI__GCF_000384235.1:WP_028485431.1 5 FVAGNWKMHGSKASVEALMAGLIKQADQAGAAKIAVCPPSLYIDQVVTALRnagcENIAVGAQNMTTEp 73 699**********************9999999**************99887544558*******98754 PP TIGR00419 65 ksGaftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere... 130 +sGaftGe+sA mlkd+G+++v++gHsErR++++e++e++++kv ++ e +l++++C+getl+ere lcl|NCBI__GCF_000384235.1:WP_028485431.1 74 DSGAFTGEVSARMLKDVGCEFVILGHSERRAMFAETNEVVAEKVKTALENDLTPILCIGETLAEREagk 142 8*****************************************************************888 PP TIGR00419 131 ....aartinnvattaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrv 195 ++++++v+ ++ A+ + v+A+EPv++iGtGk++s +a++v++++r l+k +++vae+v + lcl|NCBI__GCF_000384235.1:WP_028485431.1 143 leavISEQVEAVLSVVGIDAFAKIVIAYEPVWAIGTGKTASADQAQEVHAFIRGQLAKSNPQVAEKVVI 211 88777789999999999999************************************************* PP TIGR00419 196 lyGasvtaaedaelaaqldvdGvLlasavlkae 228 +yG+s++ +++el+aq+d+dG L+++a+lkae lcl|NCBI__GCF_000384235.1:WP_028485431.1 212 QYGGSMKPVNAQELMAQPDIDGGLIGGASLKAE 244 *******************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (255 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 5.80 // [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