Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate 15383 b1263 bifunctional indole-3-glycerol-phosphate synthase/anthranilate phosphoribosyltransferase (NCBI)
Query= SwissProt::P00900 (193 letters) >FitnessBrowser__Keio:15383 Length = 531 Score = 318 bits (815), Expect = 1e-91 Identities = 157/193 (81%), Positives = 167/193 (86%) Query: 1 MADILLLDNVDSFTYNLVDQLRASGHQVVIYRNQIGAEVIIERLQHMEQPVLMLSPGPGT 60 MADILLLDN+DSFTYNL DQLR++GH VVIYRN I A+ +IERL M PVLMLSPGPG Sbjct: 1 MADILLLDNIDSFTYNLADQLRSNGHNVVIYRNHIPAQTLIERLATMSNPVLMLSPGPGV 60 Query: 61 PSEAGCMPELLQRLRGQLPIIGICLGHQAIVEAYGGQVGQAGEILHGKASAIAHDGEGMF 120 PSEAGCMPELL RLRG+LPIIGICLGHQAIVEAYGG VGQAGEILHGKAS+I HDG+ MF Sbjct: 61 PSEAGCMPELLTRLRGKLPIIGICLGHQAIVEAYGGYVGQAGEILHGKASSIEHDGQAMF 120 Query: 121 AGMANPLPVARYHSLVGSNIPADLTVNARSGEMVMAVRDDRRRVCGFQFHPESILTTHGA 180 AG+ NPLPVARYHSLVGSNIPA LT+NA MVMAVR D RVCGFQFHPESILTT GA Sbjct: 121 AGLTNPLPVARYHSLVGSNIPAGLTINAHFNGMVMAVRHDADRVCGFQFHPESILTTQGA 180 Query: 181 RLLEQTLAWALAK 193 RLLEQTLAWA K Sbjct: 181 RLLEQTLAWAQQK 193 Lambda K H 0.322 0.138 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: 381 Number of extensions: 13 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: 193 Length of database: 531 Length adjustment: 27 Effective length of query: 166 Effective length of database: 504 Effective search space: 83664 Effective search space used: 83664 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 (21.9 bits) S2: 48 (23.1 bits)
Align candidate 15383 b1263 (bifunctional indole-3-glycerol-phosphate synthase/anthranilate phosphoribosyltransferase (NCBI))
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.3460.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-58 183.4 0.0 3.3e-58 182.7 0.0 1.4 1 lcl|FitnessBrowser__Keio:15383 b1263 bifunctional indole-3-glyc Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:15383 b1263 bifunctional indole-3-glycerol-phosphate synthase/anthranilate phosphoribosyltr # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 182.7 0.0 3.3e-58 3.3e-58 2 189 .. 4 186 .. 3 189 .. 0.95 Alignments for each domain: == domain 1 score: 182.7 bits; conditional E-value: 3.3e-58 TIGR00566 2 vllidnydsftynlvqlleelgaevvvkrndsltlqeieallplls..ivisPGPctPdeaaissleliehlaGklPil 78 +ll+dn dsftynl ++l +g++vv+ rn+ + ie+l++ + +++sPGP+ P ea+ el+ +l GklPi+ lcl|FitnessBrowser__Keio:15383 4 ILLLDNIDSFTYNLADQLRSNGHNVVIYRNHIPAQTLIERLATMSNpvLMLSPGPGVPSEAGCM-PELLTRLRGKLPII 81 8****************************************98877789*************98.9************* PP TIGR00566 79 GvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetldtllevtaleeeeiei 157 G+ClGhqa+ a G+ v +a ++ hGk s+ieh+g+a+fagl+nP l+++ryhslv ++++ l+++a + + lcl|FitnessBrowser__Keio:15383 82 GICLGHQAIVEAYGGYVGQAGEILHGKASSIEHDGQAMFAGLTNP--LPVARYHSLV--GSNIPAGLTINAHFNGM--V 154 *********************************************..*********8..578****9999987665..* PP TIGR00566 158 mairhrdlpleGvqfhPesilselGkellanf 189 ma+rh + + G qfhPesil+ +G++ll+ lcl|FitnessBrowser__Keio:15383 155 MAVRHDADRVCGFQFHPESILTTQGARLLEQT 186 ****************************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (531 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 14.97 // [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