Align anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized)
to candidate WP_044408625.1 NA59_RS04450 type 1 glutamine amidotransferase
Query= BRENDA::P20576 (201 letters) >NCBI__GCF_000934765.1:WP_044408625.1 Length = 195 Score = 305 bits (781), Expect = 4e-88 Identities = 142/192 (73%), Positives = 166/192 (86%) Query: 1 MLLMIDNYDSFTYNLVQYFGELKAEVKVVRNDELSVEQIEALAPERIVLSPGPCTPNEAG 60 MLLMIDNYDSFTYNLVQYFGEL EV V RND++++EQI L P+ +V+SPGPCTPNEAG Sbjct: 1 MLLMIDNYDSFTYNLVQYFGELGQEVVVYRNDQITLEQIVELKPDYLVISPGPCTPNEAG 60 Query: 61 VSLAVIERFAGKLPLLGVCLGHQSIGQAFGGEVVRARQVMHGKTSPIHHKDLGVFAGLAN 120 +S+ I FAGKLP+LGVCLGHQSIGQAFGG ++RA+QVMHGKTSP+ H +LGVFA L N Sbjct: 61 ISIEAIHHFAGKLPILGVCLGHQSIGQAFGGHIIRAKQVMHGKTSPVFHHNLGVFANLPN 120 Query: 121 PLTVTRYHSLVVKRESLPECLEVTAWTQHADGSLDEIMGVRHKTLNVEGVQFHPESILTE 180 P+ TRYHSLV+++ SLP+CLEVTAWTQ A G +DEIMGVRHKTL +EGVQFHPESILTE Sbjct: 121 PVETTRYHSLVIEQSSLPDCLEVTAWTQTAAGEIDEIMGVRHKTLPIEGVQFHPESILTE 180 Query: 181 QGHELLANFLRQ 192 QGH++L NFL Q Sbjct: 181 QGHKMLQNFLEQ 192 Lambda K H 0.319 0.137 0.403 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: 223 Number of extensions: 5 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: 201 Length of database: 195 Length adjustment: 20 Effective length of query: 181 Effective length of database: 175 Effective search space: 31675 Effective search space used: 31675 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 (21.7 bits) S2: 45 (21.9 bits)
Align candidate WP_044408625.1 NA59_RS04450 (type 1 glutamine amidotransferase)
to HMM TIGR00566 (glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase)
# 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/TIGR00566.hmm # target sequence database: /tmp/gapView.9323.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00566 [M=192] Accession: TIGR00566 Description: trpG_papA: glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-89 283.3 0.3 5.1e-89 283.2 0.3 1.0 1 lcl|NCBI__GCF_000934765.1:WP_044408625.1 NA59_RS04450 type 1 glutamine am Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000934765.1:WP_044408625.1 NA59_RS04450 type 1 glutamine amidotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 283.2 0.3 5.1e-89 5.1e-89 1 191 [. 1 191 [. 1 192 [. 0.98 Alignments for each domain: == domain 1 score: 283.2 bits; conditional E-value: 5.1e-89 TIGR00566 1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaisslelie 69 m+l+idnydsftynlvq++ elg+evvv rnd++tl++i +l+p+ +visPGPctP+ea+is +e+i+ lcl|NCBI__GCF_000934765.1:WP_044408625.1 1 MLLMIDNYDSFTYNLVQYFGELGQEVVVYRNDQITLEQIVELKPDY-LVISPGPCTPNEAGIS-IEAIH 67 79********************************************.****************.***** PP TIGR00566 70 hlaGklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvvea 138 h+aGklPilGvClGhq+++qafG++++ra++v+hGk+s + h++ +vfa l nP +++tryhslv+e lcl|NCBI__GCF_000934765.1:WP_044408625.1 68 HFAGKLPILGVCLGHQSIGQAFGGHIIRAKQVMHGKTSPVFHHNLGVFANLPNP--VETTRYHSLVIEQ 134 ******************************************************..************* PP TIGR00566 139 etldtllevtaleeee....ieimairhrdlpleGvqfhPesilselGkellanflk 191 +l+++levta++++ +eim++rh+ lp+eGvqfhPesil+e+G+++l+nfl+ lcl|NCBI__GCF_000934765.1:WP_044408625.1 135 SSLPDCLEVTAWTQTAageiDEIMGVRHKTLPIEGVQFHPESILTEQGHKMLQNFLE 191 *************99878889**********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (195 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: 6.18 // [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