Align Xylose isomerase (EC 5.3.1.5) (characterized)
to candidate N515DRAFT_3229 N515DRAFT_3229 D-xylose isomerase (EC 5.3.1.5)
Query= reanno::BFirm:BPHYT_RS32825 (440 letters) >FitnessBrowser__Dyella79:N515DRAFT_3229 Length = 438 Score = 680 bits (1755), Expect = 0.0 Identities = 313/437 (71%), Positives = 372/437 (85%) Query: 1 MSYFEHIPEIRYEGPQSDNPLAYRHYDKSKKVLGKTLEEHLRIAVCYWHTFVWPGVDIFG 60 MSYFEH+ IRY G ++D+PLA+RHYD S+ +LGK ++EHLR+AVCYWH+FVWPG+D+FG Sbjct: 1 MSYFEHVAPIRYAGAKTDDPLAFRHYDPSRVILGKRMDEHLRLAVCYWHSFVWPGMDMFG 60 Query: 61 QGTFRRPWQQAGDAMERAQQKADSAFEFFSKLGTPYYTFHDTDVSPEGSNLKEYSENFLR 120 GTF+RPWQQAGD M +A KAD+AF+FF +LG P+YTFHDTDV+PEG+NL EYS NF Sbjct: 61 AGTFQRPWQQAGDLMAQAHAKADAAFDFFQRLGAPFYTFHDTDVAPEGANLAEYSRNFAA 120 Query: 121 ITDYLARKQESTGIKLLWGTANLFSHPRYAAGAATSPDPEVFAFAATQVRHALDATQRLG 180 + D L KQ TG+KLLWGTANLFSHPRYAAGAA+SP PEVFA+AA+QV HA+ AT RLG Sbjct: 121 MVDVLEAKQAQTGMKLLWGTANLFSHPRYAAGAASSPQPEVFAYAASQVFHAMGATHRLG 180 Query: 181 GDNYVLWGGREGYDTLLNTDLVRERDQLARFLHMVVDHAHKIGFKGSLLIEPKPQEPTKH 240 G NYVLWGGREGYDTLLNTDL RER QL RF MVV+H HK+GF+G++LIEPKPQEPTKH Sbjct: 181 GANYVLWGGREGYDTLLNTDLRRERAQLGRFFQMVVEHKHKLGFQGTILIEPKPQEPTKH 240 Query: 241 QYDYDVATVHGFLLQHGLDKEIRVNIEANHATLAGHSFHHEIATAYALGIFGSVDANRGD 300 QYDYD ATV+GFL + GL++E++VN+EANHATLAGHSFHHE+ATA +LG+FGS+DANRGD Sbjct: 241 QYDYDTATVYGFLKEFGLEREVKVNLEANHATLAGHSFHHEVATAISLGVFGSIDANRGD 300 Query: 301 PQNGWDTDQFPNSVEELTLAFYEILKHGGFTTGGMNFDSKVRRQSVDPEDLFYGHIGAID 360 PQNGWDTDQFPNSVEELTL YEIL+ GGFTTGG NFD+KVRRQSVD DLF+GH+GAID Sbjct: 301 PQNGWDTDQFPNSVEELTLVMYEILQAGGFTTGGFNFDTKVRRQSVDAADLFHGHVGAID 360 Query: 361 NLALAVERAAVLIENDRLDQFKRQRYSGWDAEFGRKISSGDYSLSALAEEAMARGLNPQH 420 LALA+ERAA +I++DRL FK QRY+GWDA G++I G Y+L ALA+EA R L P H Sbjct: 361 ALALALERAAKMIDDDRLAAFKAQRYAGWDAGLGQQILDGGYTLQALADEAAKRDLRPGH 420 Query: 421 ASGHQELMENIVNQAIY 437 SG QE +EN+VN+ IY Sbjct: 421 VSGQQERLENLVNRYIY 437 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: 755 Number of extensions: 20 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: 440 Length of database: 438 Length adjustment: 32 Effective length of query: 408 Effective length of database: 406 Effective search space: 165648 Effective search space used: 165648 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 N515DRAFT_3229 N515DRAFT_3229 (D-xylose isomerase (EC 5.3.1.5))
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.14866.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-204 665.8 0.3 1.7e-204 665.6 0.3 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_3229 N515DRAFT_3229 D-xylose isomeras Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_3229 N515DRAFT_3229 D-xylose isomerase (EC 5.3.1.5) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 665.6 0.3 1.7e-204 1.7e-204 1 435 [] 3 436 .. 3 436 .. 1.00 Alignments for each domain: == domain 1 score: 665.6 bits; conditional E-value: 1.7e-204 TIGR02630 1 ffeeiekvkyeGkdsknplafkyynpeeviegkkmkdhlrfavayWhtlaaegaDpfGagtaerpw 66 +fe+++ ++y+G ++++plaf++y+p +vi gk+m +hlr av+yWh++ + g D+fGagt++rpw lcl|FitnessBrowser__Dyella79:N515DRAFT_3229 3 YFEHVAPIRYAGAKTDDPLAFRHYDPSRVILGKRMDEHLRLAVCYWHSFVWPGMDMFGAGTFQRPW 68 8***************************************************************** PP TIGR02630 67 dkeltdaldkakakvdaafelleklgveyycfhDvDiapegaslketnanldeivdllkekqketg 132 ++ d +++a+ak+daaf+++++lg+++y+fhD+D+apega+l+e+++n+ ++vd+l+ kq++tg lcl|FitnessBrowser__Dyella79:N515DRAFT_3229 69 QQ-AGDLMAQAHAKADAAFDFFQRLGAPFYTFHDTDVAPEGANLAEYSRNFAAMVDVLEAKQAQTG 133 96.69************************************************************* PP TIGR02630 133 vklLWgtanlfshpryvaGaatspdadvfayaaaqvkkalevtkklggenyvfWGGreGyetLlnt 198 +klLWgtanlfshpry+aGaa sp+++vfayaa+qv +a+ +t++lgg nyv+WGGreGy+tLlnt lcl|FitnessBrowser__Dyella79:N515DRAFT_3229 134 MKLLWGTANLFSHPRYAAGAASSPQPEVFAYAASQVFHAMGATHRLGGANYVLWGGREGYDTLLNT 199 ****************************************************************** PP TIGR02630 199 dlkleldnlarflklavdyakkigfkgqlliePkPkePtkhqyDfDaatvlaflkkydLdkdfkln 264 dl++e+ +l+rf++++v++++k+gf+g++liePkP+ePtkhqyD+D+atv++flk+++L++++k+n lcl|FitnessBrowser__Dyella79:N515DRAFT_3229 200 DLRRERAQLGRFFQMVVEHKHKLGFQGTILIEPKPQEPTKHQYDYDTATVYGFLKEFGLEREVKVN 265 ****************************************************************** PP TIGR02630 265 ieanhatLaghtfehelrvarelgllGsiDanrgdlllGWDtDefptdvyeatlamyevlkaggla 330 +eanhatLagh+f+he+++a +lg++GsiDanrgd ++GWDtD+fp++v+e+tl+mye+l+agg++ lcl|FitnessBrowser__Dyella79:N515DRAFT_3229 266 LEANHATLAGHSFHHEVATAISLGVFGSIDANRGDPQNGWDTDQFPNSVEELTLVMYEILQAGGFT 331 ****************************************************************** PP TIGR02630 331 kGGlnfdakvrresldaeDlllahiagmDafarglkvaaklledgaleklveeryesfdseiGkei 396 +GG+nfd kvrr+s+da Dl+++h++++Da+a++l+ aak+++d++l ++ ++ry+++d ++G++i lcl|FitnessBrowser__Dyella79:N515DRAFT_3229 332 TGGFNFDTKVRRQSVDAADLFHGHVGAIDALALALERAAKMIDDDRLAAFKAQRYAGWDAGLGQQI 397 ****************************************************************** PP TIGR02630 397 eegkadleelekyalekeeeaekksgrqelleslinkyl 435 ++g +l+ l+++a++++ ++ + sg+qe le+l+n+y+ lcl|FitnessBrowser__Dyella79:N515DRAFT_3229 398 LDGGYTLQALADEAAKRDLRPGHVSGQQERLENLVNRYI 436 *************************************97 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: 11.22 // [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