Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_038018662.1 G579_RS0106565 hypothetical protein
Query= curated2:P05378 (462 letters) >NCBI__GCF_000423825.1:WP_038018662.1 Length = 452 Score = 241 bits (616), Expect = 3e-68 Identities = 168/430 (39%), Positives = 228/430 (53%), Gaps = 21/430 (4%) Query: 35 LESV-ERGRQSRFSIVGVGARRTFRLKDGVFTVNGERV--ETRDPLRALYERVYAPLERH 91 LESV R R+SI+ L + G+ + +T L L ++ AP Sbjct: 27 LESVAHNARTGRYSILFAFPEAALWLDRQGRSWRGDALLPDTARFLDELDRQLLAPAPAE 86 Query: 92 PDLPPFFGGVVGYAAYDLVRYYERLPSLKPDDLGLPDLLFVEPEVVAVFDHLKNLLHLVA 151 P PF GG Y Y+ ++ E + + P D LP + V DH+ HLVA Sbjct: 87 PCPLPFCGGHFVYLGYEFLQQIEDI-RIPPADGALPVAFALPVRGAIVLDHVAGQGHLVA 145 Query: 152 PGRDP----EEAEARLFWAERRLKGPLPGVPGERAGGRARFQADFSREAYLEAVRRALDY 207 G D E+ A L ER +PG Q D +L+ V+R +Y Sbjct: 146 SGPDAAALLEQMAADLAALER--------MPGYAPVRLLELQED-PEAWFLDGVQRIQEY 196 Query: 208 IRAGDIFQVVLSLRLSSPLTVH--PFALYRALRSVNPSPYMGYLDLGEVVLVSASPESLL 265 IRAGD+FQV LS + + P ALY+ LR NP+P+ G+ + ++S+SPE LL Sbjct: 197 IRAGDVFQVNLSRAWQARVAGERAPLALYQQLRLHNPAPFAGFFQWRDSYVLSSSPERLL 256 Query: 266 RSDGRRVVTRPIAGTRPRGKDEEEDKRLAEELLRDEKEVAEHVMLLDLSRNDIGRVAAFG 325 + DG + +RPIAGTRPR +D ELL KE AEH+ML+DL RND+GRV G Sbjct: 257 QRDGGLLQSRPIAGTRPR--HPHQDAATTRELLAHPKERAEHIMLIDLIRNDLGRVCRPG 314 Query: 326 TVRVLEPLHVEHYSHVMHLVSTVEGILAEGKTPLDALASVLPMGTVSGAPKIRAMEIIEE 385 ++ V E + +E Y HV H+VS V G TP LA++ P GT++G PK+R MEII E Sbjct: 315 SIAVDELMVIESYRHVHHIVSNVCGAPRAEATPGQMLAALFPGGTITGCPKVRCMEIIGE 374 Query: 386 LEPHRRGPYGGSFGYLAYDGAMDMALTLRTFVVAKGWMHVQAGAGIVADSVPEREYEECW 445 LE RGPY GS GY++ DG MD + +R+ + + ++AGAGIVADSVP RE EE Sbjct: 375 LERVGRGPYTGSMGYVSVDGKMDFNILIRSMQYHQDTLRLRAGAGIVADSVPARELEETR 434 Query: 446 NKARALLKAV 455 KA LL+A+ Sbjct: 435 AKAAGLLRAL 444 Lambda K H 0.321 0.139 0.408 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: 570 Number of extensions: 30 Number of successful extensions: 4 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: 462 Length of database: 452 Length adjustment: 33 Effective length of query: 429 Effective length of database: 419 Effective search space: 179751 Effective search space used: 179751 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 (21.8 bits) S2: 51 (24.3 bits)
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