Align Aspartate--ammonia ligase; Asparagine synthetase A; EC 6.3.1.1 (characterized)
to candidate WP_012543301.1 KVAR_RS25450 asparagine synthetase A
Query= SwissProt::P00963 (330 letters) >NCBI__GCF_000025465.1:WP_012543301.1 Length = 330 Score = 603 bits (1554), Expect = e-177 Identities = 297/330 (90%), Positives = 312/330 (94%) Query: 1 MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGCEKAVQVKVK 60 MKTAYIAKQRQISFVKSHFSRQLEE+LGLIEVQAPILSRVGDGTQDNLSGCEKAVQVKVK Sbjct: 1 MKTAYIAKQRQISFVKSHFSRQLEEKLGLIEVQAPILSRVGDGTQDNLSGCEKAVQVKVK 60 Query: 61 ALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWE 120 LPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRL+P+HSVYVDQWDWE Sbjct: 61 TLPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLTPIHSVYVDQWDWE 120 Query: 121 RVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDL 180 RVMGD ER TLK+TVEAI+AGIKATE AVS+EFGL PFLP+QIHFVHSQELLSRYPDL Sbjct: 121 RVMGDEERHVGTLKATVEAIYAGIKATELAVSQEFGLKPFLPEQIHFVHSQELLSRYPDL 180 Query: 181 DAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWN 240 DAKGRERAIAK+LGAVFL+GIGGKLS+G RHDVRAPDYDDWST G AGLNGDILVWN Sbjct: 181 DAKGRERAIAKELGAVFLIGIGGKLSNGKRHDVRAPDYDDWSTEVSEGFAGLNGDILVWN 240 Query: 241 PVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRL 300 PVLEDAFE+SSMGIRVDA+ LK QLA+TGDEDRL+LEWHQALLRGEMPQTIGGGIGQSRL Sbjct: 241 PVLEDAFEISSMGIRVDAEALKRQLAVTGDEDRLQLEWHQALLRGEMPQTIGGGIGQSRL 300 Query: 301 TMLLLQLPHIGQVQCGVWPAAVRESVPSLL 330 TMLLLQL HIGQVQCGVWPA VRESV +LL Sbjct: 301 TMLLLQLDHIGQVQCGVWPAQVRESVSALL 330 Lambda K H 0.318 0.136 0.410 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: 544 Number of extensions: 9 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: 330 Length of database: 330 Length adjustment: 28 Effective length of query: 302 Effective length of database: 302 Effective search space: 91204 Effective search space used: 91204 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: 49 (23.5 bits)
Align candidate WP_012543301.1 KVAR_RS25450 (asparagine synthetase A)
to HMM TIGR00669 (asnA: aspartate--ammonia ligase (EC 6.3.1.1))
# 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.aa/TIGR00669.hmm # target sequence database: /tmp/gapView.26112.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00669 [M=330] Accession: TIGR00669 Description: asnA: aspartate--ammonia ligase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-196 638.1 0.4 1.7e-196 638.0 0.4 1.0 1 lcl|NCBI__GCF_000025465.1:WP_012543301.1 KVAR_RS25450 asparagine syntheta Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025465.1:WP_012543301.1 KVAR_RS25450 asparagine synthetase A # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 638.0 0.4 1.7e-196 1.7e-196 1 330 [] 1 330 [] 1 330 [] 1.00 Alignments for each domain: == domain 1 score: 638.0 bits; conditional E-value: 1.7e-196 TIGR00669 1 mkkafilkqqeisfvkstftqklierlglievqgpilsqvgdgiqdnlsgiekavqvkvkaipdaafev 69 mk+a+i+kq++isfvks+f+++l+e+lglievq+pils+vgdg+qdnlsg+ekavqvkvk++pda+fev lcl|NCBI__GCF_000025465.1:WP_012543301.1 1 MKTAYIAKQRQISFVKSHFSRQLEEKLGLIEVQAPILSRVGDGTQDNLSGCEKAVQVKVKTLPDAQFEV 69 9******************************************************************** PP TIGR00669 70 vhslakwkrhtlarydfkedeglfvhmkalrpdedsldpvrsvyvdqwdwekvvpegernlaylketve 138 vhslakwkr+tl+++df+++egl++hmkalrpded+l p++svyvdqwdwe+v+++ er++ +lk tve lcl|NCBI__GCF_000025465.1:WP_012543301.1 70 VHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLTPIHSVYVDQWDWERVMGDEERHVGTLKATVE 138 ********************************************************************* PP TIGR00669 139 aiyaairatevavserfglaallpkqivfvhseelvkrypdldskgredaiakelgavfligiggklsd 207 aiya+i+ate+avs++fgl+++lp+qi+fvhs+el++rypdld+kgre+aiakelgavfligiggkls+ lcl|NCBI__GCF_000025465.1:WP_012543301.1 139 AIYAGIKATELAVSQEFGLKPFLPEQIHFVHSQELLSRYPDLDAKGRERAIAKELGAVFLIGIGGKLSN 207 ********************************************************************* PP TIGR00669 208 gkphdvrapdyddwtteselgykglngdilvwnpvlgkafelssmgirvdedalrlqlaltgdedrlel 276 gk+hdvrapdyddw+te +g++glngdilvwnpvl++afe+ssmgirvd++al++qla+tgdedrl+l lcl|NCBI__GCF_000025465.1:WP_012543301.1 208 GKRHDVRAPDYDDWSTEVSEGFAGLNGDILVWNPVLEDAFEISSMGIRVDAEALKRQLAVTGDEDRLQL 276 ********************************************************************* PP TIGR00669 277 ewhqdllngklpqtigggigqsrlamlllqkkhigevqasvwpkevreevenil 330 ewhq+ll+g++pqtigggigqsrl+mlllq +hig+vq++vwp++vre+v+++l lcl|NCBI__GCF_000025465.1:WP_012543301.1 277 EWHQALLRGEMPQTIGGGIGQSRLTMLLLQLDHIGQVQCGVWPAQVRESVSALL 330 **************************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (330 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9.75 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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