Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_043767302.1 U743_RS08580 triose-phosphate isomerase
Query= BRENDA::P0A858 (255 letters) >NCBI__GCF_000733765.1:WP_043767302.1 Length = 254 Score = 233 bits (595), Expect = 2e-66 Identities = 129/251 (51%), Positives = 162/251 (64%), Gaps = 6/251 (2%) Query: 2 RHPLVMGNWKLNGSRHMVHELVSNLRKELAGV--AGCAVAIAPPEMYIDMAKREAEGSHI 59 R PLV NWK++G R L R+ +A AG V I PP Y+ + GS Sbjct: 3 RKPLVAANWKMHGDRAFGEALA---RETVASCDDAGVDVVICPPICYLTLVAGPLSGSGC 59 Query: 60 MLGAQNVDLNL-SGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKE 118 LGAQ++ + SGA TG+ + AML D GA ++I+GHSERR E +E +A KF ++ Sbjct: 60 ALGAQDLSPVVESGAHTGDINGAMLIDCGASHVIVGHSERRATRGEDNEAVAAKFLAAQQ 119 Query: 119 QGLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSA 178 GLTP+LC+GET AE + +TE V Q+DAV+ G AAF AVIAYEPVWAIGTG++A Sbjct: 120 AGLTPILCVGETLAERDGERTEAVLEAQLDAVVAAAGIAAFSRAVIAYEPVWAIGTGRTA 179 Query: 179 TPAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLK 238 +P QAQA H +R +A+ DA IA+ V I YGGSV NAA LFAQPD+DG L+GGASLK Sbjct: 180 SPDQAQAAHAALRATLARDDARIADSVRIVYGGSVKPDNAASLFAQPDVDGGLIGGASLK 239 Query: 239 ADAFAVIVKAA 249 A FA IV AA Sbjct: 240 AADFAAIVHAA 250 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: 198 Number of extensions: 9 Number of successful extensions: 3 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: 254 Length adjustment: 24 Effective length of query: 231 Effective length of database: 230 Effective search space: 53130 Effective search space used: 53130 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_043767302.1 U743_RS08580 (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.525877.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-64 204.2 1.0 1.5e-64 204.0 1.0 1.0 1 NCBI__GCF_000733765.1:WP_043767302.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000733765.1:WP_043767302.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 204.0 1.0 1.5e-64 1.5e-64 1 227 [. 6 240 .. 6 241 .. 0.94 Alignments for each domain: == domain 1 score: 204.0 bits; conditional E-value: 1.5e-64 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvd.avksGaftG 71 lv n+K+++ + e +a+ + + agv v++ pp +l v+ ++ s ++Aq++ +v+sGa+tG NCBI__GCF_000733765.1:WP_043767302.1 6 LVAANWKMHGDRAFGE-ALARETVASCDDAGVDVVICPPICYLTLVAGPLSgSGCALGAQDLSpVVESGAHTG 77 6899***999876554.44544444457899********************99********975899****** PP TIGR00419 72 eisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartinn 137 +i+ +ml d+Ga +v++gHsErR+ e +e +++k+ +++ gl++++Cvgetl+er+ ++++ NCBI__GCF_000733765.1:WP_043767302.1 78 DINGAMLIDCGASHVIVGHSERRATRGEDNEAVAAKFLAAQQAGLTPILCVGETLAERDgerteavLEAQLDA 150 **********************************************************999999887899*** PP TIGR00419 138 vattaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaela 210 v a++aA++ +v+A+EPv++iGtG+++s+ +a++ ++ +r l++ ++ +a+svr++yG+sv+ ++a l+ NCBI__GCF_000733765.1:WP_043767302.1 151 VVAAAGIAAFSRAVIAYEPVWAIGTGRTASPDQAQAAHAALRATLARDDARIADSVRIVYGGSVKPDNAASLF 223 ************************************************************************* PP TIGR00419 211 aqldvdGvLlasavlka 227 aq+dvdG L+++a+lka NCBI__GCF_000733765.1:WP_043767302.1 224 AQPDVDGGLIGGASLKA 240 ****************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (254 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: 17.04 // [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