Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_026608555.1 METAC_RS0121190 aminodeoxychorismate synthase, component I
Query= curated2:P05378 (462 letters) >NCBI__GCF_000427445.1:WP_026608555.1 Length = 454 Score = 279 bits (714), Expect = 1e-79 Identities = 180/437 (41%), Positives = 241/437 (55%), Gaps = 17/437 (3%) Query: 31 VSFLLESVERGRQSRFSIVGVGARRTFRLKDGVFTVNGERVETRDPLRALYERVYAPLER 90 ++FL ++ G+ R+S V V +++D +E L A Y +E Sbjct: 24 LTFLDSAMADGKLGRYSFVAVDPFAKLQVRDADIGW----IERLKSLLAQYR-----IEP 74 Query: 91 HPDLPPFFGGVVGYAAYDLVRYYERLPSLKPDDLGLPDLLFVEPEVVAVFDHLKN---LL 147 P LPPF GG G +Y+L R ERLP D+L PDL +VVA FD L+ +L Sbjct: 75 TPGLPPFQGGAAGLFSYELGRSLERLPKPALDELEFPDLSLGLYDVVAAFDALERRGFIL 134 Query: 148 HLVAPGRDPEEAEARLFWAERRLKGPLPGVPGERAGGR---ARFQADFSREAYLEAVRRA 204 P DP R R L+ L R G + + ++F+R Y AV Sbjct: 135 STGLPEMDPAARRRRAVERGRWLESELGRDAVSRPAGNISLSGWTSNFTRSGYERAVGEV 194 Query: 205 LDYIRAGDIFQVVLSLRL--SSPLTVHPFALYRALRSVNPSPYMGYLDLGEVVLVSASPE 262 ++ I AGDIFQ LS R ++P F YR LR VNP+P+ YLD + V+ SASPE Sbjct: 195 IERILAGDIFQANLSQRFLAAAPDDFDHFGFYRHLRKVNPAPFAAYLDHADFVIASASPE 254 Query: 263 SLLRSDGRRVVTRPIAGTRPRGKDEEEDKRLAEELLRDEKEVAEHVMLLDLSRNDIGRVA 322 LR +G RV TRPI GTRPR D D A+ L K+ AE+VM++DL RND+ RV Sbjct: 255 RFLRLEGDRVETRPIKGTRPRFADAFLDSIQAQALRESRKDRAENVMIVDLLRNDLSRVC 314 Query: 323 AFGTVRVLEPLHVEHYSHVMHLVSTVEGILAEGKTPLDALASVLPMGTVSGAPKIRAMEI 382 G+V+V + +E +S V HLVS+V G L EG+ +D LA+ P G+++GAPK+RAMEI Sbjct: 315 LPGSVQVPQLCGLETFSSVHHLVSSVVGRLREGQGAVDLLAAAFPGGSITGAPKLRAMEI 374 Query: 383 IEELEPHRRGPYGGSFGYLAYDGAMDMALTLRTFVVAKGWMHVQAGAGIVADSVPEREYE 442 I ELE H RGPY G+ GY+ +DGAMD + +RT KG VQAG GIV S P EY+ Sbjct: 375 ITELEGHARGPYCGAIGYIGFDGAMDTNIVIRTASFRKGACVVQAGGGIVTASSPAAEYD 434 Query: 443 ECWNKARALLKAVEMAE 459 E +KAR + +A + E Sbjct: 435 ETLDKARRIFEAFGVKE 451 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: 543 Number of extensions: 31 Number of successful extensions: 3 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: 454 Length adjustment: 33 Effective length of query: 429 Effective length of database: 421 Effective search space: 180609 Effective search space used: 180609 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