Align Anthranilate synthase component II (characterized, see rationale)
to candidate WP_011188120.1 DP_RS04425 aminodeoxychorismate/anthranilate synthase component II
Query= uniprot:Q8AAD4_BACTN (188 letters) >NCBI__GCF_000025945.1:WP_011188120.1 Length = 192 Score = 171 bits (432), Expect = 1e-47 Identities = 82/185 (44%), Positives = 121/185 (65%) Query: 2 KILLLDNYDSFTYNLLHAVKELGATDVEVVRNDQINLDEVERFDKIILSPGPGIPEEAGL 61 KI+LLDN DSFTYN++ ++ + V+ +++++E++++D II+SPGP +P++ Sbjct: 5 KIVLLDNNDSFTYNIVDYLRGMTEVQFRVINTHELDIEELDKYDGIIISPGPELPKDFPK 64 Query: 62 LLPIIKRYAPTKSILGVCLGHQAIGEAFGARLENLKEVYHGVQTPISILQKDVLFEGLGK 121 L +++RY TK ILG+CLGHQAI + FGA L V HG P+ +L+ D LF GL + Sbjct: 65 LFEVLQRYHRTKPILGICLGHQAIAQFFGADLSQQLPVVHGQAVPMQVLRDDSLFSGLPR 124 Query: 122 EIPVGRYHSWVVSREGFPECLEITAESQEGQIMALRHKTYDVHGIQFHPESVLTPQGKEI 181 E VG YHSW+V + P L +TA S G IMA+R + GIQFHPES +T G +I Sbjct: 125 EFRVGLYHSWLVDPKTIPARLVVTALSARGVIMAIRVTDLPIWGIQFHPESHITEHGLKI 184 Query: 182 IKNFL 186 ++NF+ Sbjct: 185 LENFI 189 Lambda K H 0.319 0.141 0.411 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: 130 Number of extensions: 3 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: 188 Length of database: 192 Length adjustment: 20 Effective length of query: 168 Effective length of database: 172 Effective search space: 28896 Effective search space used: 28896 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: 44 (21.6 bits)
Align candidate WP_011188120.1 DP_RS04425 (aminodeoxychorismate/anthranilate synthase component II)
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.1259893.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-51 160.5 0.0 2.4e-51 160.3 0.0 1.0 1 NCBI__GCF_000025945.1:WP_011188120.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000025945.1:WP_011188120.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 160.3 0.0 2.4e-51 2.4e-51 2 191 .. 6 190 .. 5 191 .. 0.91 Alignments for each domain: == domain 1 score: 160.3 bits; conditional E-value: 2.4e-51 TIGR00566 2 vllidnydsftynlvqlleelga.evvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaG 73 ++l+dn dsftyn+v++l +++ + v ++l +ie+l i+isPGP P++ e+++++ NCBI__GCF_000025945.1:WP_011188120.1 6 IVLLDNNDSFTYNIVDYLRGMTEvQFRVINTHEL---DIEELDKYDGIIISPGPELPKDFPKL-FEVLQRYHR 74 889***************9998524556666666...556666667799**********9887.9******** PP TIGR00566 74 klPilGvClGhqalaqafGadvvraekvkhGkvseie.hngaavfaglfnPdalkatryhslvveaetldtll 145 PilG+ClGhqa+aq fGad+++ v hG+ ++ + + ++f gl P+ ++++ yhs v+++t+++ l NCBI__GCF_000025945.1:WP_011188120.1 75 TKPILGICLGHQAIAQFFGADLSQQLPVVHGQAVPMQvLRDDSLFSGL--PREFRVGLYHSWLVDPKTIPARL 145 ************************************845788999999..777******************** PP TIGR00566 146 evtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191 vtal+ + imair dlp+ G+qfhPes ++e+G ++l+nf+k NCBI__GCF_000025945.1:WP_011188120.1 146 VVTALSARG-VIMAIRVTDLPIWGIQFHPESHITEHGLKILENFIK 190 *******99.**********************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (192 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: 13.85 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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