Align xylose isomerase (EC 5.3.1.5) (characterized)
to candidate 350321 BT0793 xylose isomerase (NCBI ptt file)
Query= BRENDA::Q8A9M2 (438 letters) >FitnessBrowser__Btheta:350321 Length = 438 Score = 898 bits (2321), Expect = 0.0 Identities = 438/438 (100%), Positives = 438/438 (100%) Query: 1 MATKEFFPGIEKIKFEGKDSKNPMAFRYYDAEKVINGKKMKDWLRFAMAWWHTLCAEGGD 60 MATKEFFPGIEKIKFEGKDSKNPMAFRYYDAEKVINGKKMKDWLRFAMAWWHTLCAEGGD Sbjct: 1 MATKEFFPGIEKIKFEGKDSKNPMAFRYYDAEKVINGKKMKDWLRFAMAWWHTLCAEGGD 60 Query: 61 QFGGGTKQFPWNGNADAIQAAKDKMDAGFEFMQKMGIEYYCFHDVDLVSEGASVEEYEAN 120 QFGGGTKQFPWNGNADAIQAAKDKMDAGFEFMQKMGIEYYCFHDVDLVSEGASVEEYEAN Sbjct: 61 QFGGGTKQFPWNGNADAIQAAKDKMDAGFEFMQKMGIEYYCFHDVDLVSEGASVEEYEAN 120 Query: 121 LKEIVAYAKQKQAETGIKLLWGTANVFGHARYMNGAATNPDFDVVARAAVQIKNAIDATI 180 LKEIVAYAKQKQAETGIKLLWGTANVFGHARYMNGAATNPDFDVVARAAVQIKNAIDATI Sbjct: 121 LKEIVAYAKQKQAETGIKLLWGTANVFGHARYMNGAATNPDFDVVARAAVQIKNAIDATI 180 Query: 181 ELGGENYVFWGGREGYMSLLNTDQKREKEHLAQMLTIARDYARARGFKGTFLIEPKPMEP 240 ELGGENYVFWGGREGYMSLLNTDQKREKEHLAQMLTIARDYARARGFKGTFLIEPKPMEP Sbjct: 181 ELGGENYVFWGGREGYMSLLNTDQKREKEHLAQMLTIARDYARARGFKGTFLIEPKPMEP 240 Query: 241 TKHQYDVDTETVIGFLKAHGLDKDFKVNIEVNHATLAGHTFEHELAVAVDNGMLGSIDAN 300 TKHQYDVDTETVIGFLKAHGLDKDFKVNIEVNHATLAGHTFEHELAVAVDNGMLGSIDAN Sbjct: 241 TKHQYDVDTETVIGFLKAHGLDKDFKVNIEVNHATLAGHTFEHELAVAVDNGMLGSIDAN 300 Query: 301 RGDYQNGWDTDQFPIDNYELTQAMMQIIRNGGLGTGGTNFDAKTRRNSTDLEDIFIAHIA 360 RGDYQNGWDTDQFPIDNYELTQAMMQIIRNGGLGTGGTNFDAKTRRNSTDLEDIFIAHIA Sbjct: 301 RGDYQNGWDTDQFPIDNYELTQAMMQIIRNGGLGTGGTNFDAKTRRNSTDLEDIFIAHIA 360 Query: 361 GMDAMARALESAAALLDESPYKKMLADRYASFDGGKGKEFEDGKLTLEDVVAYAKTKGEP 420 GMDAMARALESAAALLDESPYKKMLADRYASFDGGKGKEFEDGKLTLEDVVAYAKTKGEP Sbjct: 361 GMDAMARALESAAALLDESPYKKMLADRYASFDGGKGKEFEDGKLTLEDVVAYAKTKGEP 420 Query: 421 KQTSGKQELYEAILNMYC 438 KQTSGKQELYEAILNMYC Sbjct: 421 KQTSGKQELYEAILNMYC 438 Lambda K H 0.317 0.134 0.402 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: 884 Number of extensions: 26 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: 438 Length of database: 438 Length adjustment: 32 Effective length of query: 406 Effective length of database: 406 Effective search space: 164836 Effective search space used: 164836 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: 51 (24.3 bits)
Align candidate 350321 BT0793 (xylose isomerase (NCBI ptt file))
to HMM TIGR02630 (xylA: xylose isomerase (EC 5.3.1.5))
# 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/TIGR02630.hmm # target sequence database: /tmp/gapView.5957.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02630 [M=435] Accession: TIGR02630 Description: xylose_isom_A: xylose 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-218 710.9 8.6 3.3e-218 710.8 8.6 1.0 1 lcl|FitnessBrowser__Btheta:350321 BT0793 xylose isomerase (NCBI pt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:350321 BT0793 xylose isomerase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 710.8 8.6 3.3e-218 3.3e-218 1 435 [] 6 438 .] 6 438 .] 0.99 Alignments for each domain: == domain 1 score: 710.8 bits; conditional E-value: 3.3e-218 TIGR02630 1 ffeeiekvkyeGkdsknplafkyynpeeviegkkmkdhlrfavayWhtlaaegaDpfGagtaerpwdkeltdaldk 76 ff++iek+k+eGkdsknp+af+yy++e+vi+gkkmkd+lrfa+a+Whtl+aeg+D+fG+gt+++pw+ ++da+++ lcl|FitnessBrowser__Btheta:350321 6 FFPGIEKIKFEGKDSKNPMAFRYYDAEKVINGKKMKDWLRFAMAWWHTLCAEGGDQFGGGTKQFPWNG-NADAIQA 80 89*****************************************************************6.59***** PP TIGR02630 77 akakvdaafelleklgveyycfhDvDiapegaslketnanldeivdllkekqketgvklLWgtanlfshpryvaGa 152 ak+k+da fe+++k+g+eyycfhDvD+++egas++e++anl+eiv ++k+kq+etg+klLWgtan+f h+ry++Ga lcl|FitnessBrowser__Btheta:350321 81 AKDKMDAGFEFMQKMGIEYYCFHDVDLVSEGASVEEYEANLKEIVAYAKQKQAETGIKLLWGTANVFGHARYMNGA 156 **************************************************************************** PP TIGR02630 153 atspdadvfayaaaqvkkalevtkklggenyvfWGGreGyetLlntdlkleldnlarflklavdyakkigfkgqll 228 at+pd+dv+a+aa+q+k+a+++t +lggenyvfWGGreGy++Llntd+k+e+++la++l++a+dya+ gfkg++l lcl|FitnessBrowser__Btheta:350321 157 ATNPDFDVVARAAVQIKNAIDATIELGGENYVFWGGREGYMSLLNTDQKREKEHLAQMLTIARDYARARGFKGTFL 232 **************************************************************************** PP TIGR02630 229 iePkPkePtkhqyDfDaatvlaflkkydLdkdfklnieanhatLaghtfehelrvarelgllGsiDanrgdlllGW 304 iePkP+ePtkhqyD+D++tv++flk+++Ldkdfk+nie+nhatLaghtfehel+va ++g+lGsiDanrgd+++GW lcl|FitnessBrowser__Btheta:350321 233 IEPKPMEPTKHQYDVDTETVIGFLKAHGLDKDFKVNIEVNHATLAGHTFEHELAVAVDNGMLGSIDANRGDYQNGW 308 **************************************************************************** PP TIGR02630 305 DtDefptdvyeatlamyevlkagglakGGlnfdakvrresldaeDlllahiagmDafarglkvaaklledgalekl 380 DtD+fp+d ye+t+am++++++ggl++GG+nfdak+rr+s+d eD+++ahiagmDa+ar+l++aa+ll+++ ++k+ lcl|FitnessBrowser__Btheta:350321 309 DTDQFPIDNYELTQAMMQIIRNGGLGTGGTNFDAKTRRNSTDLEDIFIAHIAGMDAMARALESAAALLDESPYKKM 384 **************************************************************************** PP TIGR02630 381 veeryesfdseiGkeieegkadleelekyalekeeeaekksgrqelleslinkyl 435 +++ry+sfd + Gke+e+gk +le++ +ya++k+e ++++sg+qel+e+++n+y+ lcl|FitnessBrowser__Btheta:350321 385 LADRYASFDGGKGKEFEDGKLTLEDVVAYAKTKGE-PKQTSGKQELYEAILNMYC 438 *********************************97.****************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (435 nodes) Target sequences: 1 (438 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: 10.46 // [ok]
This GapMind analysis is from Sep 17 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