Align Probable glucosamine-6-phosphate deaminase 2; GlcN6P deaminase 2; GNPDA 2; Glucosamine-6-phosphate isomerase 2; EC 3.5.99.6 (characterized)
to candidate WP_086511255.1 BZY95_RS17935 glucosamine-6-phosphate deaminase
Query= SwissProt::O31458 (249 letters) >NCBI__GCF_002151265.1:WP_086511255.1 Length = 258 Score = 241 bits (616), Expect = 8e-69 Identities = 120/246 (48%), Positives = 169/246 (68%), Gaps = 2/246 (0%) Query: 1 MKILIAEHYEELCKLSAAIIKEQIQAKKDAVLGLATGSTPVGLYKQLISDYQAGEIDFSK 60 M ++I + E + +L A II++Q+ AK D+VLGLATG+TP+ LY++L+ +QA + + Sbjct: 1 MDLIIVHNVERMAQLGANIIQQQLSAKPDSVLGLATGATPLALYRELVVRHQATRLTLDQ 60 Query: 61 VTTFNLDEYAGLSPSHPQSYNHFMHEHLFQHINMQPDHIHIPQGDNPQLEAACKVYEDLI 120 +TTFNLDEY GL P HP SY H+M HLF + + P H+P G P +A + YE + Sbjct: 61 LTTFNLDEYLGLGPDHPASYAHYMRRHLFGPLQLDPQRTHLPDGLAPDPQAEARRYEAQL 120 Query: 121 RQAGGIDVQILGIGANGHIGFNEPGSDFEDRTRVVKLSESTIQANARFFGGDPVLVPRLA 180 + AGG+D+Q+LGIG NGHIGFNEPGS + RTRVV+LS +T+ AN R F D + P A Sbjct: 121 QAAGGVDLQLLGIGLNGHIGFNEPGSPLDSRTRVVRLSATTLAANRRHFPADAEM-PTHA 179 Query: 181 ISMGIKTIMEFSKHIVLLASGEEKADAIQKMAEGPVTTDVPASILQKHNHVTVIADYKAA 240 I++GI I+E ++H++LLA+G KA A+ + EGPVT +PAS+LQ+H +V+VI D AA Sbjct: 180 ITLGIGNILE-ARHLLLLATGRAKARAVAEALEGPVTATLPASVLQRHPNVSVILDAAAA 238 Query: 241 QKLKSA 246 L A Sbjct: 239 AALSPA 244 Lambda K H 0.317 0.134 0.382 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: 196 Number of extensions: 7 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: 249 Length of database: 258 Length adjustment: 24 Effective length of query: 225 Effective length of database: 234 Effective search space: 52650 Effective search space used: 52650 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
Align candidate WP_086511255.1 BZY95_RS17935 (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.31147.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-85 272.1 0.0 2.6e-85 271.9 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086511255.1 BZY95_RS17935 glucosamine-6-phos Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086511255.1 BZY95_RS17935 glucosamine-6-phosphate deaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 271.9 0.0 2.6e-85 2.6e-85 1 248 [. 1 242 [. 1 250 [. 0.98 Alignments for each domain: == domain 1 score: 271.9 bits; conditional E-value: 2.6e-85 TIGR00502 1 mklliletyeelsklaariiaekinefkpdaerpfvlGlatGgtPvglykqlielykagkvsfkkvvtf 69 m l+i+++ e +++l a+ii++++ + kpd vlGlatG+tP+ ly++l+ ++a ++ +++++tf lcl|NCBI__GCF_002151265.1:WP_086511255.1 1 MDLIIVHNVERMAQLGANIIQQQLSA-KPD-S---VLGLATGATPLALYRELVVRHQATRLTLDQLTTF 64 889***********************.999.5...9********************************* PP TIGR00502 70 nldeyvglseehPesyhsfmyenffqhidikpeninilnGnaddleaecrryeekikslGkidlfllGi 138 nldey+gl ++hP sy ++m +++f +++ p++ ++++G a+d +ae rrye +++ +G++dl+llGi lcl|NCBI__GCF_002151265.1:WP_086511255.1 65 NLDEYLGLGPDHPASYAHYMRRHLFGPLQLDPQRTHLPDGLAPDPQAEARRYEAQLQAAGGVDLQLLGI 133 ********************************************************************* PP TIGR00502 139 GadGhiafnePgsslesrtrvktltedtiiansrffegdvnkvPkkaltvGiktildskevlllvsGke 207 G +Ghi+fnePgs l+srtrv++l+ t+ an r+f++d ++P +a+t+Gi+ il+++++lll++G+ lcl|NCBI__GCF_002151265.1:WP_086511255.1 134 GLNGHIGFNEPGSPLDSRTRVVRLSATTLAANRRHFPADA-EMPTHAITLGIGNILEARHLLLLATGRA 201 *************************************886.68************************** PP TIGR00502 208 kaeavkklvegsvnedvtisalqlhkkvivvadeeaaqelk 248 ka+av +++eg+v+ ++++s+lq h +v v+ d +aa l lcl|NCBI__GCF_002151265.1:WP_086511255.1 202 KARAVAEALEGPVTATLPASVLQRHPNVSVILDAAAAAALS 242 ***********************************998775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (259 nodes) Target sequences: 1 (258 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: 9.93 // [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