Align xylose isomerase (EC 5.3.1.5) (characterized)
to candidate WP_013403911.1 CALHY_RS10405 xylose isomerase
Query= BRENDA::D2DK62 (438 letters) >NCBI__GCF_000166355.1:WP_013403911.1 Length = 438 Score = 798 bits (2061), Expect = 0.0 Identities = 377/438 (86%), Positives = 416/438 (94%) Query: 1 MEYFKNVPQIKYEGPKSNNPYAFKFYNPDEIIDGKPLKEHLRFSVAYWHTFTANGTDPFG 60 M+YFK++P +KYEGP+S+NP+AFK+YNPDEIIDGKPLK+HLRF+VAYWHTF A G DPFG Sbjct: 1 MKYFKDIPGVKYEGPQSDNPFAFKYYNPDEIIDGKPLKDHLRFAVAYWHTFCATGADPFG 60 Query: 61 APTMQRPWNHLSDPMDIAKARVEAAFEFFEKLDVPFFCFHDRDIAPEGENLRETNKNLDT 120 PT+ RPW+ S+PMD AKARVEAAFEFFEKL+VPFFCFHDRDIAPEGENLRETNKNLD Sbjct: 61 QPTIVRPWDRFSNPMDNAKARVEAAFEFFEKLNVPFFCFHDRDIAPEGENLRETNKNLDE 120 Query: 121 IVAMIKDYLKTSKTKVLWGTANLFSNPRFVHGAATSCNADVFAYAAAQVKKALEITKELG 180 IV+MIK+YLKTSKTKVLWGTANLFS+PR+VHGAATSCNADVFAYAAAQVKKALE+TKELG Sbjct: 121 IVSMIKEYLKTSKTKVLWGTANLFSHPRYVHGAATSCNADVFAYAAAQVKKALEVTKELG 180 Query: 181 GQNYVFWGGREGYETLLNTDMELELDNLARFLHMAVEYAKEIGFEGQLLIEPKPKEPTKH 240 G+NYVFWGGREGYETLLNTDMELELDNLARFL MAV+YAKEIGF+GQ LIEPKPKEPTKH Sbjct: 181 GENYVFWGGREGYETLLNTDMELELDNLARFLRMAVDYAKEIGFDGQFLIEPKPKEPTKH 240 Query: 241 QYDFDAANVYAFLKKYDLDKYFKLNIEANHATLAGHDFQHELRYARINNMLGSIDANMGD 300 QYDFDAA+VY FLKKYDLDKYFKLNIE NHATLAGHDF HELR+ARINNMLGSIDANMGD Sbjct: 241 QYDFDAAHVYGFLKKYDLDKYFKLNIEVNHATLAGHDFHHELRFARINNMLGSIDANMGD 300 Query: 301 MLLGWDTDQFPTDIRMTTLAMYEVIKMGGFDKGGLNFDAKVRRASFEPEDLFLGHIAGMD 360 +LLGWDTDQFPTD+R+TTLAMYEVIKMGGFDKGGLNFDAKVRR SFE EDL +GHIAGMD Sbjct: 301 LLLGWDTDQFPTDVRLTTLAMYEVIKMGGFDKGGLNFDAKVRRGSFELEDLVIGHIAGMD 360 Query: 361 AFAKGFKVAYKLVKDGVFDRFIEERYKSYREGIGAEIVSGKANFKTLEEYALNNPKIENK 420 AFAKGFK+AYKLVK+GVFD+FI+ERYKSY+EGIGA+IVSG+ANFK LEEYAL+ KIENK Sbjct: 361 AFAKGFKIAYKLVKNGVFDKFIDERYKSYKEGIGAKIVSGEANFKMLEEYALSLDKIENK 420 Query: 421 SGKQELLESILNQYLFSE 438 SGKQELLE ILN+Y+F+E Sbjct: 421 SGKQELLEMILNKYMFTE 438 Lambda K H 0.320 0.137 0.413 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: 830 Number of extensions: 27 Number of successful extensions: 1 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
Align candidate WP_013403911.1 CALHY_RS10405 (xylose isomerase)
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.2530906.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-230 751.7 2.7 1.4e-230 751.6 2.7 1.0 1 NCBI__GCF_000166355.1:WP_013403911.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166355.1:WP_013403911.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 751.6 2.7 1.4e-230 1.4e-230 1 435 [] 3 435 .. 3 435 .. 0.99 Alignments for each domain: == domain 1 score: 751.6 bits; conditional E-value: 1.4e-230 TIGR02630 1 ffeeiekvkyeGkdsknplafkyynpeeviegkkmkdhlrfavayWhtlaaegaDpfGagtaerpwdkeltda 73 +f++i vkyeG++s+np+afkyynp+e+i+gk +kdhlrfavayWht++a+gaDpfG+ t+ rpwd + +++ NCBI__GCF_000166355.1:WP_013403911.1 3 YFKDIPGVKYEGPQSDNPFAFKYYNPDEIIDGKPLKDHLRFAVAYWHTFCATGADPFGQPTIVRPWD-RFSNP 74 8*****************************************************************9.68*** PP TIGR02630 74 ldkakakvdaafelleklgveyycfhDvDiapegaslketnanldeivdllkekqketgvklLWgtanlfshp 146 +d+aka+v+aafe++ekl+v+++cfhD+Diapeg++l+etn+nldeiv+++ke+ k+++ k+LWgtanlfshp NCBI__GCF_000166355.1:WP_013403911.1 75 MDNAKARVEAAFEFFEKLNVPFFCFHDRDIAPEGENLRETNKNLDEIVSMIKEYLKTSKTKVLWGTANLFSHP 147 ************************************************************************* PP TIGR02630 147 ryvaGaatspdadvfayaaaqvkkalevtkklggenyvfWGGreGyetLlntdlkleldnlarflklavdyak 219 ryv+Gaats++advfayaaaqvkkalevtk+lggenyvfWGGreGyetLlntd++leldnlarfl++avdyak NCBI__GCF_000166355.1:WP_013403911.1 148 RYVHGAATSCNADVFAYAAAQVKKALEVTKELGGENYVFWGGREGYETLLNTDMELELDNLARFLRMAVDYAK 220 ************************************************************************* PP TIGR02630 220 kigfkgqlliePkPkePtkhqyDfDaatvlaflkkydLdkdfklnieanhatLaghtfehelrvarelgllGs 292 +igf+gq+liePkPkePtkhqyDfDaa v++flkkydLdk+fklnie+nhatLagh f+helr ar +++lGs NCBI__GCF_000166355.1:WP_013403911.1 221 EIGFDGQFLIEPKPKEPTKHQYDFDAAHVYGFLKKYDLDKYFKLNIEVNHATLAGHDFHHELRFARINNMLGS 293 ************************************************************************* PP TIGR02630 293 iDanrgdlllGWDtDefptdvyeatlamyevlkagglakGGlnfdakvrresldaeDlllahiagmDafargl 365 iDan gdlllGWDtD+fptdv +tlamyev+k gg++kGGlnfdakvrr s++ eDl+++hiagmDafa+g+ NCBI__GCF_000166355.1:WP_013403911.1 294 IDANMGDLLLGWDTDQFPTDVRLTTLAMYEVIKMGGFDKGGLNFDAKVRRGSFELEDLVIGHIAGMDAFAKGF 366 ************************************************************************* PP TIGR02630 366 kvaaklledgaleklveeryesfdseiGkeieegkadleelekyalekeeeaekksgrqelleslinkyl 435 k+a+kl+++g+++k+++ery+s++++iG++i++g+a+++ le+yal+ ++ +e+ksg+qelle+++nky+ NCBI__GCF_000166355.1:WP_013403911.1 367 KIAYKLVKNGVFDKFIDERYKSYKEGIGAKIVSGEANFKMLEEYALSLDK-IENKSGKQELLEMILNKYM 435 ************************************************87.*****************96 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 14.39 // [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