Align Glucosamine-6-phosphate deaminase (EC 3.5.99.6) (characterized)
to candidate WP_008991223.1 I215_RS06780 glucosamine-6-phosphate deaminase
Query= reanno::Pedo557:CA265_RS21925 (641 letters) >NCBI__GCF_000300875.1:WP_008991223.1 Length = 638 Score = 748 bits (1932), Expect = 0.0 Identities = 368/632 (58%), Positives = 466/632 (73%), Gaps = 7/632 (1%) Query: 8 EETRFEKLPVSVFENPKIASINVAHRIAELIKSKQANNTPAVLGLATGVTPIAVYAELVR 67 E+T+FEK+ +FE+ AS VA IA+LI+ KQ VLGLATG +PI VY ELVR Sbjct: 14 EDTKFEKIHNEIFEDSYEASKVVAAEIADLIRQKQDKGEACVLGLATGSSPIKVYEELVR 73 Query: 68 LHKEEGLSFKNVITFNLDEYYPMAPTAAQSYVTFMNENLFNHIDIDKKNVHIPDGTLALE 127 LHK LSF NVITFNLDEYYPM QSY FM+++LF+HIDI+ +N+HIP G ++ E Sbjct: 74 LHKNGELSFHNVITFNLDEYYPMDAENRQSYYYFMHQHLFDHIDINPENIHIPSGQVSQE 133 Query: 128 DIPAFCLEYEKKIGDLGGLDIQILGIGRTGHIGFNEPGSAPNSGTRLVTLDDLTRRDAAR 187 ++ +C++Y+ KI LGGLD Q+LGIGRTGHIGFNEPGS NSGTR++TLD +TRRDAA Sbjct: 134 ELNQYCIDYDMKIKQLGGLDFQLLGIGRTGHIGFNEPGSHINSGTRIITLDHITRRDAAS 193 Query: 188 DFGGKTFVPTKAITMGIGTIFKAREIILMAWSRKKASIIKKAVEGEISGDVPATFLQLSD 247 DF G VP KAITMG+ TI K++ II++AW KKASIIK+ VEG+I+ +PA+FLQ Sbjct: 194 DFNGIENVPKKAITMGVSTILKSKRIIMLAWGHKKASIIKETVEGQITATIPASFLQNHP 253 Query: 248 HVEFILDAPAASELTRFYTPWLVKDCVWTDALIRKAVIWLANTLKKPILKLTEDDYNNNG 307 + I+D AASEL+R TPW+V CVWTD L KAV WL+ LKKP+LKLT+ DYN +G Sbjct: 254 NTTMIMDQEAASELSRIKTPWIVSQCVWTDNLKLKAVTWLSEELKKPVLKLTDKDYNEHG 313 Query: 308 MAQLATEKGPVYNINIHIFNKLQHTITGWPGGKPNADDSQRPERAEPAKKRVIIFSPHPD 367 M+ L + +G YN+NI IFNKLQHTITGWPGGKPNADD+ RPER P KKR+IIFSPHPD Sbjct: 314 MSGLLSIEGSSYNLNIKIFNKLQHTITGWPGGKPNADDTNRPERKSPEKKRIIIFSPHPD 373 Query: 368 DDVISMGGTFLRLVDQGHDVHVAYQTSGNTAVWDDDALRFVEFNVDFTEKMGMDNTHLKD 427 DDVISMGGTF RL++QGHDVHVAYQTSGN AV D++AL+F E V + T+ K Sbjct: 374 DDVISMGGTFSRLIEQGHDVHVAYQTSGNIAVTDEEALKFAE--VANLLSPSTEETNFK- 430 Query: 428 LYNKMRAFIEQKKPNQIDTPEIQTVKGLIRKGEAIAGARYCGLEDDHIHFQALPFYESGK 487 K+ +F+ K D+ E + VKGLIR+ E+ RY GL+D +HF LPFYE+G+ Sbjct: 431 ---KIISFLNSKTTAYGDSLETRKVKGLIRRMESYGATRYLGLDDSKVHFLDLPFYETGE 487 Query: 488 VQKNPVTDADIELTIELLQKVKPQQVYAAGDFEDPHGTHIVCFNIILEALKRLRKTEAWA 547 V+KNPV DI+L +L+ ++P Q+YAAGD DPHGTH +C + I E+L ++ + + Sbjct: 488 VKKNPVGPEDIQLISDLITTIQPHQIYAAGDLADPHGTHKLCLDAIFESLASIKHLD-FM 546 Query: 548 QDCWLWMYRGAWHEFETHEIEMAVPISPQELERKKYAIFKHQSQKDRAVFPGDDSREFWQ 607 DCW+W+YRGAWHE++ +IEMAVP+SP E+ +K AI HQSQKDR +F G+DSREFW Sbjct: 547 DDCWVWLYRGAWHEWDIADIEMAVPLSPDEMNKKINAILFHQSQKDRVMFQGEDSREFWV 606 Query: 608 RAEDRNRDTAKAYDELGLAEYEAMEAFVRWKF 639 RA++RNR+TA YD LGLAEYEA+EAF R+ F Sbjct: 607 RAQERNRNTALLYDNLGLAEYEAIEAFKRYHF 638 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: 1128 Number of extensions: 33 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: 638 Length adjustment: 38 Effective length of query: 603 Effective length of database: 600 Effective search space: 361800 Effective search space used: 361800 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_008991223.1 I215_RS06780 (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.3409792.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-88 281.5 0.3 5.2e-88 280.7 0.3 1.3 1 NCBI__GCF_000300875.1:WP_008991223.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000300875.1:WP_008991223.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 280.7 0.3 5.2e-88 5.2e-88 10 248 .. 30 268 .. 24 275 .. 0.95 Alignments for each domain: == domain 1 score: 280.7 bits; conditional E-value: 5.2e-88 TIGR00502 10 eelsklaariiaekinefkpdaerpfvlGlatGgtPvglykqlielykagkvsfkkvvtfnldeyvglseehP 82 e sk+ a+ ia+ i++ k+d+ + vlGlatG++P+++y++l++l+k+g++sf++v+tfnldey ++ e+ NCBI__GCF_000300875.1:WP_008991223.1 30 YEASKVVAAEIADLIRQ-KQDKGEACVLGLATGSSPIKVYEELVRLHKNGELSFHNVITFNLDEYYPMDAENR 101 57899************.999999************************************************* PP TIGR00502 83 esyhsfmyenffqhidikpeninilnGnad..dleaecrryeekikslGkidlfllGiGadGhiafnePgssl 153 +sy++fm++++f+hidi+peni+i+ G+ + +l++ c y+ kik+lG++d +llGiG+ Ghi+fnePgs + NCBI__GCF_000300875.1:WP_008991223.1 102 QSYYYFMHQHLFDHIDINPENIHIPSGQVSqeELNQYCIDYDMKIKQLGGLDFQLLGIGRTGHIGFNEPGSHI 174 ***************************8651168899************************************ PP TIGR00502 154 esrtrvktltedtiiansrffegdvnkvPkkaltvGiktildskevlllvsGkekaeavkklvegsvnedvti 226 +s tr+ tl + t+ + f+ +++vPkka+t+G+ til+sk++++l+ G++ka+ +k+ veg+++ ++++ NCBI__GCF_000300875.1:WP_008991223.1 175 NSGTRIITLDHITRRDAASDFN-GIENVPKKAITMGVSTILKSKRIIMLAWGHKKASIIKETVEGQITATIPA 246 **************99998898.7************************************************* PP TIGR00502 227 salqlhkkvivvadeeaaqelk 248 s lq h + ++++d+eaa+el NCBI__GCF_000300875.1:WP_008991223.1 247 SFLQNHPNTTMIMDQEAASELS 268 ******************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (259 nodes) Target sequences: 1 (638 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 43.24 // [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