Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate BWI76_RS11855 BWI76_RS11855 bifunctional glutamine amidotransferase/anthranilate phosphoribosyltransferase
Query= SwissProt::P00900 (193 letters) >FitnessBrowser__Koxy:BWI76_RS11855 Length = 531 Score = 320 bits (820), Expect = 3e-92 Identities = 156/193 (80%), Positives = 171/193 (88%) Query: 1 MADILLLDNVDSFTYNLVDQLRASGHQVVIYRNQIGAEVIIERLQHMEQPVLMLSPGPGT 60 MADILLLDN+DSFTYNL DQLR++GH VVIYRN + A+ +IER+ M+ PVLMLSPGPGT Sbjct: 1 MADILLLDNIDSFTYNLADQLRSNGHNVVIYRNSVPAQALIERIGTMKNPVLMLSPGPGT 60 Query: 61 PSEAGCMPELLQRLRGQLPIIGICLGHQAIVEAYGGQVGQAGEILHGKASAIAHDGEGMF 120 PSEAGCMPELL R+RG+LPIIGICLGHQAIVEAYGG VGQAGEILHGKAS+I HDG+ MF Sbjct: 61 PSEAGCMPELLIRMRGKLPIIGICLGHQAIVEAYGGYVGQAGEILHGKASSIEHDGQAMF 120 Query: 121 AGMANPLPVARYHSLVGSNIPADLTVNARSGEMVMAVRDDRRRVCGFQFHPESILTTHGA 180 AG++NPLPVARYHSLVGSNIPA LT+NA MVMAVR D RVCGFQFHPESILTT GA Sbjct: 121 AGLSNPLPVARYHSLVGSNIPAGLTINAHFNGMVMAVRHDADRVCGFQFHPESILTTQGA 180 Query: 181 RLLEQTLAWALAK 193 RLLEQTLAWAL K Sbjct: 181 RLLEQTLAWALQK 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: 377 Number of extensions: 14 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 BWI76_RS11855 BWI76_RS11855 (bifunctional glutamine amidotransferase/anthranilate phosphoribosyltransferase)
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.11212.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-57 179.7 0.0 4.4e-57 179.0 0.0 1.4 1 lcl|FitnessBrowser__Koxy:BWI76_RS11855 BWI76_RS11855 bifunctional gluta Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS11855 BWI76_RS11855 bifunctional glutamine amidotransferase/anthranilate phosphorib # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 179.0 0.0 4.4e-57 4.4e-57 2 189 .. 4 186 .. 3 189 .. 0.95 Alignments for each domain: == domain 1 score: 179.0 bits; conditional E-value: 4.4e-57 TIGR00566 2 vllidnydsftynlvqlleelgaevvvkrndsltlqeieallplls..ivisPGPctPdeaaisslelieh 70 +ll+dn dsftynl ++l +g++vv+ rn + ie++ + ++ +++sPGP+tP ea+ el+ + lcl|FitnessBrowser__Koxy:BWI76_RS11855 4 ILLLDNIDSFTYNLADQLRSNGHNVVIYRNSVPAQALIERIGTMKNpvLMLSPGPGTPSEAGCM-PELLIR 73 8******************************999999999988877779*************98.9***** PP TIGR00566 71 laGklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetl 141 + GklPi+G+ClGhqa+ a G+ v +a ++ hGk s+ieh+g+a+fagl+nP l+++ryhslv ++ lcl|FitnessBrowser__Koxy:BWI76_RS11855 74 MRGKLPIIGICLGHQAIVEAYGGYVGQAGEILHGKASSIEHDGQAMFAGLSNP--LPVARYHSLV--GSNI 140 *****************************************************..*********8..578* PP TIGR00566 142 dtllevtaleeeeieimairhrdlpleGvqfhPesilselGkellanf 189 ++ l+++a + +ma+rh + + G qfhPesil+ +G++ll+ lcl|FitnessBrowser__Koxy:BWI76_RS11855 141 PAGLTINAHFNGM--VMAVRHDADRVCGFQFHPESILTTQGARLLEQT 186 ***9999987665..*****************************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: 18.51 // [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