Align Glucosamine-6-phosphate deaminase 1; GlcN6P deaminase 1; GNPDA 1; Glucosamine-6-phosphate isomerase 1; EC 3.5.99.6 (characterized)
to candidate WP_008539730.1 HMPREF9454_RS10530 glucosamine-6-phosphate deaminase
Query= SwissProt::O35000 (242 letters) >NCBI__GCF_000245775.1:WP_008539730.1 Length = 251 Score = 260 bits (665), Expect = 2e-74 Identities = 118/242 (48%), Positives = 179/242 (73%) Query: 1 MKVMECQTYEELSQIAARITADTIKEKPDAVLGLATGGTPEGTYRQLIRLHQTENLSFQN 60 M+++ +YEE+S++AARI A + KP++VLGLATG TPEG Y L+++HQ+ L F Sbjct: 1 MRIIVTDSYEEMSKVAARIVAGQLYLKPNSVLGLATGSTPEGMYANLVKVHQSVGLDFSE 60 Query: 61 ITTVNLDEYAGLSSDDPNSYHFYMNDRFFQHIDSKPSRHFIPNGNADDLEAECRRYEQLV 120 + + NLDEY GL ++ SY+++M+ F H++ KP IPNGN ++LE EC++Y++L+ Sbjct: 61 VISFNLDEYIGLDKENEQSYYYFMHKHLFDHVNIKPENIHIPNGNPENLEEECKKYDKLI 120 Query: 121 DSLGDTDIQLLGIGRNGHIGFNEPGTSFKSRTHVVTLNEQTRQANARYFPSIDSVPKKAL 180 ++ G D+Q+LGIG+N HIGFNEP F++ TH V L+E+T +AN+R+F + + VPK A+ Sbjct: 121 EAKGGIDLQVLGIGQNAHIGFNEPDIKFEATTHKVKLDEETIKANSRFFENEEDVPKYAI 180 Query: 181 TMGIQTILSSKRILLLISGKSKAEAVRKLLEGNISEDFPASALHLHSDVTVLIDREAASL 240 +MGI+TI+ +K+I+LL SGK+KAEA+ K + G++ D PAS L LH DV V++D++AASL Sbjct: 181 SMGIKTIMLAKKIILLASGKNKAEAIYKAVYGSVRPDAPASILQLHQDVVVIVDKDAASL 240 Query: 241 RP 242 P Sbjct: 241 LP 242 Lambda K H 0.316 0.133 0.375 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: 199 Number of extensions: 6 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: 242 Length of database: 251 Length adjustment: 24 Effective length of query: 218 Effective length of database: 227 Effective search space: 49486 Effective search space used: 49486 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 (21.6 bits) S2: 46 (22.3 bits)
Align candidate WP_008539730.1 HMPREF9454_RS10530 (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.868781.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-100 320.8 0.7 3.3e-100 320.7 0.7 1.0 1 NCBI__GCF_000245775.1:WP_008539730.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000245775.1:WP_008539730.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 320.7 0.7 3.3e-100 3.3e-100 1 255 [. 1 249 [. 1 251 [] 0.97 Alignments for each domain: == domain 1 score: 320.7 bits; conditional E-value: 3.3e-100 TIGR00502 1 mklliletyeelsklaariiaekinefkpdaerpfvlGlatGgtPvglykqlielykagkvsfkkvvtfnlde 73 m+++ ++ yee+sk+aari+a ++ kp+ vlGlatG+tP+g+y +l++++++ ++f++v+ fnlde NCBI__GCF_000245775.1:WP_008539730.1 1 MRIIVTDSYEEMSKVAARIVAGQLYL-KPN-S---VLGLATGSTPEGMYANLVKVHQSVGLDFSEVISFNLDE 68 9***********************97.999.5...9************************************* PP TIGR00502 74 yvglseehPesyhsfmyenffqhidikpeninilnGnaddleaecrryeekikslGkidlfllGiGadGhiaf 146 y+gl++e+ +sy++fm++++f+h++ikpeni+i+nGn ++le ec++y+++i+ G+idl++lGiG++ hi+f NCBI__GCF_000245775.1:WP_008539730.1 69 YIGLDKENEQSYYYFMHKHLFDHVNIKPENIHIPNGNPENLEEECKKYDKLIEAKGGIDLQVLGIGQNAHIGF 141 ************************************************************************* PP TIGR00502 147 nePgsslesrtrvktltedtiiansrffegdvnkvPkkaltvGiktildskevlllvsGkekaeavkklvegs 219 neP ++e t+ ++l e+ti ansrffe+ + vPk+a+++Gikti+ +k+++ll+sGk+kaea+ k+v gs NCBI__GCF_000245775.1:WP_008539730.1 142 NEPDIKFEATTHKVKLDEETIKANSRFFEN-EEDVPKYAISMGIKTIMLAKKIILLASGKNKAEAIYKAVYGS 213 *****************************6.578*************************************** PP TIGR00502 220 vnedvtisalqlhkkvivvadeeaaqelkvktlkyf 255 v d ++s+lqlh++v+v++d++aa+ l+ k k f NCBI__GCF_000245775.1:WP_008539730.1 214 VRPDAPASILQLHQDVVVIVDKDAASLLPEKDKKVF 249 **************************9998766655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (259 nodes) Target sequences: 1 (251 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: 14.46 // [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