Align Aminodeoxychorismate/anthranilate synthase component II (characterized, see rationale)
to candidate CA265_RS22895 CA265_RS22895 aminodeoxychorismate/anthranilate synthase component II
Query= uniprot:A0A1X9ZDE4_9SPHI (198 letters) >FitnessBrowser__Pedo557:CA265_RS22895 Length = 198 Score = 409 bits (1051), Expect = e-119 Identities = 198/198 (100%), Positives = 198/198 (100%) Query: 1 MEDINKKTVLVIDNYDSFTYNLVHLINEVGYEAEVWRNDKFDLADVEKYDKILLSPGPGI 60 MEDINKKTVLVIDNYDSFTYNLVHLINEVGYEAEVWRNDKFDLADVEKYDKILLSPGPGI Sbjct: 1 MEDINKKTVLVIDNYDSFTYNLVHLINEVGYEAEVWRNDKFDLADVEKYDKILLSPGPGI 60 Query: 61 PEEAGLLLDVIRTYAPTKSIFGVCLGQQAIAEVFGGTLLNLGRPMHGIATPVTVVDGDEP 120 PEEAGLLLDVIRTYAPTKSIFGVCLGQQAIAEVFGGTLLNLGRPMHGIATPVTVVDGDEP Sbjct: 61 PEEAGLLLDVIRTYAPTKSIFGVCLGQQAIAEVFGGTLLNLGRPMHGIATPVTVVDGDEP 120 Query: 121 LFWECPQTINVGRYHSWVVSKDNFPSCLKITARDHKSEIMALRHETLDVRGVQFHPESVL 180 LFWECPQTINVGRYHSWVVSKDNFPSCLKITARDHKSEIMALRHETLDVRGVQFHPESVL Sbjct: 121 LFWECPQTINVGRYHSWVVSKDNFPSCLKITARDHKSEIMALRHETLDVRGVQFHPESVL 180 Query: 181 TEYGKQMMENWLSSSTTV 198 TEYGKQMMENWLSSSTTV Sbjct: 181 TEYGKQMMENWLSSSTTV 198 Lambda K H 0.319 0.137 0.420 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: 254 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: 198 Length of database: 198 Length adjustment: 20 Effective length of query: 178 Effective length of database: 178 Effective search space: 31684 Effective search space used: 31684 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 CA265_RS22895 CA265_RS22895 (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.26196.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-58 183.5 0.0 2.1e-58 183.3 0.0 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS22895 CA265_RS22895 aminodeoxychorisma Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS22895 CA265_RS22895 aminodeoxychorismate/anthranilate synthase component II # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 183.3 0.0 2.1e-58 2.1e-58 2 191 .. 9 193 .. 8 194 .. 0.95 Alignments for each domain: == domain 1 score: 183.3 bits; conditional E-value: 2.1e-58 TIGR00566 2 vllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaisslelie 69 vl+idnydsftynlv+l++e g e v rnd++ l+++e+ + i++sPGP+ P+ea++ l++i+ lcl|FitnessBrowser__Pedo557:CA265_RS22895 9 VLVIDNYDSFTYNLVHLINEVGYEAEVWRNDKFDLADVEKYD--K-ILLSPGPGIPEEAGLL-LDVIR 72 9**************************************864..4.88*************9.***** PP TIGR00566 70 hlaGklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfn..Pdalkatryhslv 135 +a i+GvClG+qa+a +fG+ + ++ + +hG ++ + ++lf P++++++ryhs v lcl|FitnessBrowser__Pedo557:CA265_RS22895 73 TYAPTKSIFGVCLGQQAIAEVFGGTLLNLGRPMHGIATPVTVVD--GDEPLFWecPQTINVGRYHSWV 138 *****************************************998..456666556************* PP TIGR00566 136 veaetldtllevtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191 v ++ +++l++ta ++++ eima+rh+ l++ GvqfhPes+l+e Gk++++n+l lcl|FitnessBrowser__Pedo557:CA265_RS22895 139 VSKDNFPSCLKITARDHKS-EIMALRHETLDVRGVQFHPESVLTEYGKQMMENWLS 193 **************99988.*********************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (198 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: 8.77 // [ok]
This GapMind analysis is from Apr 09 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