Align Glucosamine-6-phosphate deaminase (EC 3.5.99.6) (characterized)
to candidate WP_008992130.1 I215_RS11450 glucosamine-6-phosphate deaminase
Query= reanno::Pedo557:CA265_RS21925 (641 letters) >NCBI__GCF_000300875.1:WP_008992130.1 Length = 644 Score = 751 bits (1940), Expect = 0.0 Identities = 362/632 (57%), Positives = 468/632 (74%), Gaps = 6/632 (0%) Query: 8 EETRFEKLPVSVFENPKIASINVAHRIAELIKSKQANNTPAVLGLATGVTPIAVYAELVR 67 E+ R+EK+ VFE+ AS+ VA IA+LI K VLGLATG +PI VY ELV+ Sbjct: 19 EDNRYEKIHNVVFESSSEASLLVAREIADLIVDKNNRGETCVLGLATGSSPIRVYDELVK 78 Query: 68 LHKEEGLSFKNVITFNLDEYYPMAPTAAQSYVTFMNENLFNHIDIDKKNVHIPDGTLALE 127 +H+E GLSFKNV++FNLDEY+PM P + SY FMNE+LFNHIDI K+N+ IPDGT+A + Sbjct: 79 MHRENGLSFKNVVSFNLDEYFPMNPESIHSYHHFMNEHLFNHIDIPKENIFIPDGTIAQQ 138 Query: 128 DIPAFCLEYEKKIGDLGGLDIQILGIGRTGHIGFNEPGSAPNSGTRLVTLDDLTRRDAAR 187 DIPA+C YE+KI GG+D Q+LGIGRTGHIGFNEPGS NS TR +TLD LTR DA+ Sbjct: 139 DIPAYCQGYEQKIKSFGGIDFQLLGIGRTGHIGFNEPGSHYNSITRSITLDQLTREDASS 198 Query: 188 DFGGKTFVPTKAITMGIGTIFKAREIILMAWSRKKASIIKKAVEGEISGDVPATFLQLSD 247 F G VP KAITMG+GT+F A+ I+L+AW KKA ++K+ +EGEI +PAT+LQ Sbjct: 199 GFHGIENVPKKAITMGVGTVFSAKRIVLLAWGHKKAEVVKQTIEGEILPQIPATYLQEHL 258 Query: 248 HVEFILDAPAASELTRFYTPWLVKDCVWTDALIRKAVIWLANTLKKPILKLTEDDYNNNG 307 + +L+ AAS LTRF +PWLV + W++AL+++AV+WL + K IL+LT+ DYN +G Sbjct: 259 NTTMVLNTEAASMLTRFESPWLVGEVQWSEALMKRAVVWLCRKVDKSILRLTDKDYNEHG 318 Query: 308 MAQLATEKGPVYNINIHIFNKLQHTITGWPGGKPNADDSQRPERAEPAKKRVIIFSPHPD 367 +A L TEKG Y +NI +FNKLQHTITGWPGGKPNADDS RPER P KKRVIIFSPHPD Sbjct: 319 LASLITEKGSTYQLNIDMFNKLQHTITGWPGGKPNADDSNRPERKSPEKKRVIIFSPHPD 378 Query: 368 DDVISMGGTFLRLVDQGHDVHVAYQTSGNTAVWDDDALRFVEFNVDFTEKMGMDNTHLKD 427 DDVISMGGTF RLV+QGH+VH+AYQTSGN AV + DAL+F E +DF + N D Sbjct: 379 DDVISMGGTFDRLVEQGHEVHIAYQTSGNIAVSNADALKFAEVAMDF-----LPNCKGVD 433 Query: 428 LYNKMRAFIEQKKPNQIDTPEIQTVKGLIRKGEAIAGARYCGLEDDHIHFQALPFYESGK 487 K IE ++ N+ID E++ +KGLIRK E+IA RY + D+ +HF LPFYE+G Sbjct: 434 KLQKATKAIEDQRENEIDPLEVRELKGLIRKRESIAATRYLNVPDEQVHFLNLPFYETGT 493 Query: 488 VQKNPVTDADIELTIELLQKVKPQQVYAAGDFEDPHGTHIVCFNIILEALKRLRKTEAWA 547 ++KNP++ DI + +L+ ++P QVYAAGD DPHGTH VC + + +A+ L K++++ Sbjct: 494 IKKNPLSQDDIAIVKKLISDIQPHQVYAAGDLADPHGTHKVCLDAVFKAMAEL-KSQSYM 552 Query: 548 QDCWLWMYRGAWHEFETHEIEMAVPISPQELERKKYAIFKHQSQKDRAVFPGDDSREFWQ 607 CWLW+YRGAWHE+E HEI+MAVP+SP ++ RK+ AIF HQSQKD +F G+D REFW Sbjct: 553 DQCWLWLYRGAWHEWEIHEIDMAVPMSPDQVLRKRKAIFFHQSQKDGVLFQGEDLREFWV 612 Query: 608 RAEDRNRDTAKAYDELGLAEYEAMEAFVRWKF 639 RAE+RN++TAK Y +LGLA+Y A+EAF R+ + Sbjct: 613 RAEERNKETAKHYRDLGLADYAAIEAFKRFDY 644 Lambda K H 0.319 0.136 0.412 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: 1163 Number of extensions: 40 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: 641 Length of database: 644 Length adjustment: 38 Effective length of query: 603 Effective length of database: 606 Effective search space: 365418 Effective search space used: 365418 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: 54 (25.4 bits)
Align candidate WP_008992130.1 I215_RS11450 (glucosamine-6-phosphate deaminase)
to HMM TIGR00502 (nagB: glucosamine-6-phosphate deaminase (EC 3.5.99.6))
# 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/TIGR00502.hmm # target sequence database: /tmp/gapView.1821462.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00502 [M=259] Accession: TIGR00502 Description: nagB: glucosamine-6-phosphate deaminase 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-81 259.7 0.1 2.1e-81 259.1 0.1 1.2 1 NCBI__GCF_000300875.1:WP_008992130.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000300875.1:WP_008992130.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 259.1 0.1 2.1e-81 2.1e-81 7 247 .. 32 272 .. 26 277 .. 0.95 Alignments for each domain: == domain 1 score: 259.1 bits; conditional E-value: 2.1e-81 TIGR00502 7 etyeelsklaariiaekinefkpdaerpfvlGlatGgtPvglykqlielykagkvsfkkvvtfnldeyvglse 79 e e s l ar ia+ i + k+++ + vlGlatG++P+ +y +l+++++ + +sfk+vv fnldey +++ NCBI__GCF_000300875.1:WP_008992130.1 32 ESSSEASLLVAREIADLIVD-KNNRGETCVLGLATGSSPIRVYDELVKMHRENGLSFKNVVSFNLDEYFPMNP 103 567788999***********.888899********************************************** PP TIGR00502 80 ehPesyhsfmyenffqhidikpeninilnGn..addleaecrryeekikslGkidlfllGiGadGhiafnePg 150 e +syh+fm+e++f+hidi +eni+i++G ++d+ a c+ ye+kiks+G+id +llGiG+ Ghi+fnePg NCBI__GCF_000300875.1:WP_008992130.1 104 ESIHSYHHFMNEHLFNHIDIPKENIFIPDGTiaQQDIPAYCQGYEQKIKSFGGIDFQLLGIGRTGHIGFNEPG 176 ******************************73256788*********************************** PP TIGR00502 151 sslesrtrvktltedtiiansrffegdvnkvPkkaltvGiktildskevlllvsGkekaeavkklvegsvned 223 s ++s tr tl + t+ s f+ +++vPkka+t+G++t++++k+++ll+ G++kae vk+ +eg + + NCBI__GCF_000300875.1:WP_008992130.1 177 SHYNSITRSITLDQLTREDASSGFH-GIENVPKKAITMGVGTVFSAKRIVLLAWGHKKAEVVKQTIEGEILPQ 248 *****************98888887.6********************************************** PP TIGR00502 224 vtisalqlhkkvivvadeeaaqel 247 ++++ lq h + ++v ++eaa+ l NCBI__GCF_000300875.1:WP_008992130.1 249 IPATYLQEHLNTTMVLNTEAASML 272 *******************99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (259 nodes) Target sequences: 1 (644 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 20.89 // [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