Align Glucosamine-6-phosphate deaminase (EC 3.5.99.6) (characterized)
to candidate WP_062061000.1 N456_RS19760 glucosamine-6-phosphate deaminase
Query= reanno::Pedo557:CA265_RS21925 (641 letters) >NCBI__GCF_001401755.1:WP_062061000.1 Length = 639 Score = 782 bits (2020), Expect = 0.0 Identities = 374/632 (59%), Positives = 476/632 (75%), Gaps = 6/632 (0%) Query: 8 EETRFEKLPVSVFENPKIASINVAHRIAELIKSKQANNTPAVLGLATGVTPIAVYAELVR 67 E+++FEK+ +F + IAS VA+ IA LIK KQ P VLGLATG +PI VY ELV Sbjct: 14 EKSKFEKIHSEIFPDSSIASKLVANEIATLIKQKQQEGNPCVLGLATGSSPIKVYEELVS 73 Query: 68 LHKEEGLSFKNVITFNLDEYYPMAPTAAQSYVTFMNENLFNHIDIDKKNVHIPDGTLALE 127 LH+ LSF NV+TFNLDEYYPM T QSY FM+++LF+HIDI+ +NV+IPDGT+ + Sbjct: 74 LHRSGELSFSNVVTFNLDEYYPMDSTHQQSYYHFMHQHLFDHIDINPENVNIPDGTVPIL 133 Query: 128 DIPAFCLEYEKKIGDLGGLDIQILGIGRTGHIGFNEPGSAPNSGTRLVTLDDLTRRDAAR 187 ++ +C++YE KI + GGLD Q+LGIGRTGHIGFNEPGS PNSGTR++TLD +TR DA+ Sbjct: 134 EMDQYCIDYEMKIKEYGGLDFQLLGIGRTGHIGFNEPGSHPNSGTRIITLDHVTRTDASS 193 Query: 188 DFGGKTFVPTKAITMGIGTIFKAREIILMAWSRKKASIIKKAVEGEISGDVPATFLQLSD 247 DF G VP KA+TMGI TI K+ ++L+AW KKASI+K+ +EGE+ ++PA+FLQ Sbjct: 194 DFNGLENVPKKAVTMGISTIMKSTRVLLLAWGHKKASIVKETIEGEVISNIPASFLQEHK 253 Query: 248 HVEFILDAPAASELTRFYTPWLVKDCVWTDALIRKAVIWLANTLKKPILKLTEDDYNNNG 307 + ILD+ AASELTR TPWLV C+WT+ L KAV WL+ L KP+LKLT+ DYN+NG Sbjct: 254 NTTIILDSEAASELTRIKTPWLVDQCIWTEQLKFKAVTWLSEELTKPVLKLTDKDYNDNG 313 Query: 308 MAQLATEKGPVYNINIHIFNKLQHTITGWPGGKPNADDSQRPERAEPAKKRVIIFSPHPD 367 M+ L +G YN+NI IFNKLQH+ITGWPGGKPNADD+ RPERA PAKKRV+IFSPHPD Sbjct: 314 MSSLLAVEGSSYNLNIKIFNKLQHSITGWPGGKPNADDTNRPERALPAKKRVLIFSPHPD 373 Query: 368 DDVISMGGTFLRLVDQGHDVHVAYQTSGNTAVWDDDALRFVEFNVDFTEKMGMDNTHLKD 427 DDVISMGGTFLRL+DQGHDVHV YQTSGN AV D++AL+F E F G DN+ Sbjct: 374 DDVISMGGTFLRLIDQGHDVHVVYQTSGNIAVTDEEALKFAEVANSFQSSNG-DNSS--- 429 Query: 428 LYNKMRAFIEQKKPNQIDTPEIQTVKGLIRKGEAIAGARYCGLEDDHIHFQALPFYESGK 487 Y K+ +F++ K ID E++ +KGLIR+ E+I RY GL DD +HF LPFYE+GK Sbjct: 430 -YEKVISFLKSKNQGDIDILEVRQIKGLIRRMESIGATRYFGLNDDKVHFLDLPFYETGK 488 Query: 488 VQKNPVTDADIELTIELLQKVKPQQVYAAGDFEDPHGTHIVCFNIILEALKRLRKTEAWA 547 ++KNP+ + DI++T +++K+KP Q+YAAGD DPHGTH VC + + ALK L+ E + Sbjct: 489 IKKNPLGEEDIKITESIIEKIKPHQIYAAGDLADPHGTHKVCLDAVFSALKNLKPKE-YM 547 Query: 548 QDCWLWMYRGAWHEFETHEIEMAVPISPQELERKKYAIFKHQSQKDRAVFPGDDSREFWQ 607 DCWLW+YRGAW E++ EIEMAVP+SP E+ +K AI HQSQKDR +F G+DSREFW Sbjct: 548 DDCWLWLYRGAWQEWDVSEIEMAVPLSPDEVSKKTNAILFHQSQKDRVMFQGEDSREFWL 607 Query: 608 RAEDRNRDTAKAYDELGLAEYEAMEAFVRWKF 639 RA +RNR+TAK YD+LGLA+YEA+EAF ++ F Sbjct: 608 RARERNRNTAKLYDQLGLADYEAIEAFKKYDF 639 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: 1157 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: 639 Length adjustment: 38 Effective length of query: 603 Effective length of database: 601 Effective search space: 362403 Effective search space used: 362403 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_062061000.1 N456_RS19760 (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.235527.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8e-87 276.8 0.1 1.5e-86 275.9 0.1 1.4 1 NCBI__GCF_001401755.1:WP_062061000.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001401755.1:WP_062061000.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 275.9 0.1 1.5e-86 1.5e-86 13 248 .. 33 268 .. 25 276 .. 0.96 Alignments for each domain: == domain 1 score: 275.9 bits; conditional E-value: 1.5e-86 TIGR00502 13 sklaariiaekinefkpdaerpfvlGlatGgtPvglykqlielykagkvsfkkvvtfnldeyvglseehPesy 85 skl a+ ia i++ k+++ +p vlGlatG++P+++y++l++l+++g++sf++vvtfnldey +++ h +sy NCBI__GCF_001401755.1:WP_062061000.1 33 SKLVANEIATLIKQ-KQQEGNPCVLGLATGSSPIKVYEELVSLHRSGELSFSNVVTFNLDEYYPMDSTHQQSY 104 89999999999*99.888899**************************************************** PP TIGR00502 86 hsfmyenffqhidikpeninilnGnad..dleaecrryeekikslGkidlfllGiGadGhiafnePgsslesr 156 ++fm++++f+hidi+pen+ni++G + ++++ c ye kik++G++d +llGiG+ Ghi+fnePgs +s NCBI__GCF_001401755.1:WP_062061000.1 105 YHFMHQHLFDHIDINPENVNIPDGTVPilEMDQYCIDYEMKIKEYGGLDFQLLGIGRTGHIGFNEPGSHPNSG 177 *************************994456678*************************************** PP TIGR00502 157 trvktltedtiiansrffegdvnkvPkkaltvGiktildskevlllvsGkekaeavkklvegsvnedvtisal 229 tr+ tl + t+ s f+ +++vPkka+t+Gi ti++s +vlll+ G++ka+ vk+ +eg v ++++s l NCBI__GCF_001401755.1:WP_062061000.1 178 TRIITLDHVTRTDASSDFN-GLENVPKKAVTMGISTIMKSTRVLLLAWGHKKASIVKETIEGEVISNIPASFL 249 ************9999998.799************************************************** PP TIGR00502 230 qlhkkvivvadeeaaqelk 248 q hk+ +++ d eaa+el NCBI__GCF_001401755.1:WP_062061000.1 250 QEHKNTTIILDSEAASELT 268 ***************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (259 nodes) Target sequences: 1 (639 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: 44.27 // [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