Align Xylose isomerase (EC 5.3.1.5) (characterized)
to candidate AZOBR_RS27920 AZOBR_RS27920 xylose isomerase
Query= reanno::BFirm:BPHYT_RS32825 (440 letters) >FitnessBrowser__azobra:AZOBR_RS27920 Length = 435 Score = 573 bits (1477), Expect = e-168 Identities = 270/435 (62%), Positives = 331/435 (76%), Gaps = 3/435 (0%) Query: 2 SYFEHIPEIRYEGPQSDNPLAYRHYDKSKKVLGKTLEEHLRIAVCYWHTFVWPGVDIFGQ 61 +YF + IRYEGP SD PLAYR YD + VLG+ + +HLR+AVCYWH+F WPG D FG Sbjct: 4 AYFTGVERIRYEGPDSDTPLAYRWYDPDRMVLGRRMADHLRVAVCYWHSFCWPGSDPFGG 63 Query: 62 GTFRRPWQQAGDAMERAQQKADSAFEFFSKLGTPYYTFHDTDVSPEGSNLKEYSENFLRI 121 GT RPW +AGD + A+ K D AFE F KLG P++TFHD DV+PE +L+E F R+ Sbjct: 64 GTLDRPWMRAGDPVALAEAKMDVAFELFGKLGVPFFTFHDRDVAPEMGSLRETQATFARL 123 Query: 122 TDYLARKQESTGIKLLWGTANLFSHPRYAAGAATSPDPEVFAFAATQVRHALDATQRLGG 181 T+ L E +G+KLLWGTANLFSHPRY AGAAT+PDPEVFA AA QVR AL+AT RLGG Sbjct: 124 TERLQGCIERSGVKLLWGTANLFSHPRYMAGAATNPDPEVFACAAAQVRDALEATHRLGG 183 Query: 182 DNYVLWGGREGYDTLLNTDLVRERDQLARFLHMVVDHAHKIGFKGSLLIEPKPQEPTKHQ 241 NYVLWGGREGYDTLLNTD+ RE DQL RFL MVV+H HKIGF G++LIEPKP EPTKHQ Sbjct: 184 VNYVLWGGREGYDTLLNTDMARELDQLGRFLTMVVEHKHKIGFTGTILIEPKPMEPTKHQ 243 Query: 242 YDYDVATVHGFLLQHGLDKEIRVNIEANHATLAGHSFHHEIATAYALGIFGSVDANRGDP 301 YD+DVATV+GFL ++GL+KE+ VNIE NHATLAGHSF HE+ATA ALG+FGS+D NRGDP Sbjct: 244 YDHDVATVYGFLKRYGLEKEVAVNIEVNHATLAGHSFEHEVATALALGVFGSIDMNRGDP 303 Query: 302 QNGWDTDQFPNSVEELTLAFYEILKHGGFTTGGMNFDSKVRRQSVDPEDLFYGHIGAIDN 361 QNGWDTDQFPN EL L IL+ GGFTTGG NFD+K+RRQSV+P+DL + H+G ID Sbjct: 304 QNGWDTDQFPNDHVELALPMARILESGGFTTGGFNFDAKIRRQSVEPDDLLHAHVGGIDT 363 Query: 362 LALAVERAAVLIENDRLDQFKRQRYSGWDAEFGRKISSGDYSLSALAEEAMARGLNPQHA 421 LA A+ A L+E+ RL + +RY+GW + G+K+ G L+ A+ + G +P+ Sbjct: 364 LARALLAGARLVEDGRLRSLRAERYAGWKGDLGQKLLGG-LDLAGAADAGL--GFDPRPR 420 Query: 422 SGHQELMENIVNQAI 436 SG QE++EN+VN+ + Sbjct: 421 SGRQEMLENLVNRLV 435 Lambda K H 0.319 0.136 0.414 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: 705 Number of extensions: 26 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: 440 Length of database: 435 Length adjustment: 32 Effective length of query: 408 Effective length of database: 403 Effective search space: 164424 Effective search space used: 164424 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 (21.7 bits) S2: 51 (24.3 bits)
Align candidate AZOBR_RS27920 AZOBR_RS27920 (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.26764.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-198 646.5 0.0 1.2e-198 646.3 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS27920 AZOBR_RS27920 xylose isomerase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS27920 AZOBR_RS27920 xylose isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 646.3 0.0 1.2e-198 1.2e-198 1 434 [. 5 434 .. 5 435 .] 0.98 Alignments for each domain: == domain 1 score: 646.3 bits; conditional E-value: 1.2e-198 TIGR02630 1 ffeeiekvkyeGkdsknplafkyynpeeviegkkmkdhlrfavayWhtlaaegaDpfGagtaerpwdke 69 +f+++e+++yeG+ds+ pla+++y+p++++ g++m dhlr av+yWh++++ g+DpfG+gt +rpw + lcl|FitnessBrowser__azobra:AZOBR_RS27920 5 YFTGVERIRYEGPDSDTPLAYRWYDPDRMVLGRRMADHLRVAVCYWHSFCWPGSDPFGGGTLDRPWM-R 72 89****************************************************************9.5 PP TIGR02630 70 ltdaldkakakvdaafelleklgveyycfhDvDiapegaslketnanldeivdllkekqketgvklLWg 138 d+++ a+ak+d+afel+ klgv++++fhD+D+ape sl+et+a++ ++++ l+ +++gvklLWg lcl|FitnessBrowser__azobra:AZOBR_RS27920 73 AGDPVALAEAKMDVAFELFGKLGVPFFTFHDRDVAPEMGSLRETQATFARLTERLQGCIERSGVKLLWG 141 7******************************************************************** PP TIGR02630 139 tanlfshpryvaGaatspdadvfayaaaqvkkalevtkklggenyvfWGGreGyetLlntdlkleldnl 207 tanlfshpry+aGaat+pd++vfa aaaqv+ ale+t++lgg nyv+WGGreGy+tLlntd+++eld+l lcl|FitnessBrowser__azobra:AZOBR_RS27920 142 TANLFSHPRYMAGAATNPDPEVFACAAAQVRDALEATHRLGGVNYVLWGGREGYDTLLNTDMARELDQL 210 ********************************************************************* PP TIGR02630 208 arflklavdyakkigfkgqlliePkPkePtkhqyDfDaatvlaflkkydLdkdfklnieanhatLaght 276 +rfl+++v++++kigf+g++liePkP+ePtkhqyD D+atv++flk+y+L+k++ +nie+nhatLagh+ lcl|FitnessBrowser__azobra:AZOBR_RS27920 211 GRFLTMVVEHKHKIGFTGTILIEPKPMEPTKHQYDHDVATVYGFLKRYGLEKEVAVNIEVNHATLAGHS 279 ********************************************************************* PP TIGR02630 277 fehelrvarelgllGsiDanrgdlllGWDtDefptdvyeatlamyevlkagglakGGlnfdakvrresl 345 fehe+++a +lg++GsiD+nrgd ++GWDtD+fp+d e++l m ++l++gg+++GG+nfdak+rr+s+ lcl|FitnessBrowser__azobra:AZOBR_RS27920 280 FEHEVATALALGVFGSIDMNRGDPQNGWDTDQFPNDHVELALPMARILESGGFTTGGFNFDAKIRRQSV 348 ********************************************************************* PP TIGR02630 346 daeDlllahiagmDafarglkvaaklledgaleklveeryesfdseiGkeieegkadleelekyaleke 414 +++Dll+ah++g+D++ar+l + a+l+edg+l +l +ery++++ ++G++++ g dl+ ++ l lcl|FitnessBrowser__azobra:AZOBR_RS27920 349 EPDDLLHAHVGGIDTLARALLAGARLVEDGRLRSLRAERYAGWKGDLGQKLLGG-LDLAGAADAGLGF- 415 ****************************************************98.8888888877666. PP TIGR02630 415 eeaekksgrqelleslinky 434 +++ +sgrqe+le+l+n+ lcl|FitnessBrowser__azobra:AZOBR_RS27920 416 -DPRPRSGRQEMLENLVNRL 434 .68***************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (435 nodes) Target sequences: 1 (435 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.74 // [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