Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate PP_2329 PP_2329 aminodeoxychorismate synthase / para-aminobenzoate synthase multi-enzyme complex
Query= curated2:P05378 (462 letters) >FitnessBrowser__Putida:PP_2329 Length = 446 Score = 249 bits (637), Expect = 1e-70 Identities = 165/454 (36%), Positives = 235/454 (51%), Gaps = 44/454 (9%) Query: 21 AYLKLAEKAPVSFLLESVERGRQ-SRFSIVGVGARRTFRLKDGVFTVNGERVETRDPLRA 79 AY +AP + LL+S G + RF ++ + + + + + R Sbjct: 17 AYFAHLRQAPGAILLDSARPGAERGRFDLLSA------------WPLQQLQAQPDEDGRV 64 Query: 80 LYERVYAPLER--HPDLP-----PFFGGVVGYAAYDLVRYYERLPSLKPDDLGLPDLLFV 132 +R+ A L + H DLP PF GG++GY +YD R E LPSL DDLGLPD Sbjct: 65 FLQRLRAGLAQLGHADLPNGVELPFAGGLIGYLSYDFGRRLEHLPSLAVDDLGLPDAQLG 124 Query: 133 EPEVVAVFDHLKNLLHLV---APGRDPEEAEARLFW------AERRLKGPLPGVPGERAG 183 V DHL LV + D E LF + RL P+ G Sbjct: 125 LYAWALVSDHLLGTSQLVFHPSLAGDERERLISLFQDTSATTGDFRLLAPMAG------- 177 Query: 184 GRARFQADFSREAYLEAVRRALDYIRAGDIFQVVLSLRLSSPLTVHPFALYRALRSVNPS 243 D E Y A + YI+AGD +Q+ L+ R +P P+ Y+ALR P+ Sbjct: 178 -------DLEPEQYKTAFDQVQRYIQAGDCYQINLTQRFRAPCQGDPWRAYQALRQACPT 230 Query: 244 PYMGYLDLGE-VVLVSASPESLLRSDGRRVVTRPIAGTRPRGKDEEEDKRLAEELLRDEK 302 P+ GY L + L+S SPE +R +V TRPI GTRPR D +D+R A+ELL K Sbjct: 231 PFSGYQQLADGSTLLSFSPERFIRVSQGQVETRPIKGTRPRASDPAQDQRNAQELLHSPK 290 Query: 303 EVAEHVMLLDLSRNDIGRVAAFGTVRVLEPLHVEHYSHVMHLVSTVEGILAEGKTPLDAL 362 + +E++M++DL RND+GR G+V+V E +E Y +V HLVS++ G LA K LD + Sbjct: 291 DRSENLMIVDLLRNDLGRTCEIGSVKVPELFSLESYPNVHHLVSSITGQLASDKDALDLI 350 Query: 363 ASVLPMGTVSGAPKIRAMEIIEELEPHRRGPYGGSFGYLAYDGAMDMALTLRTFVVAKGW 422 P G+++GAPKIRAM+II+ELEP RR Y GS Y+ G MD ++ +R+ ++ G Sbjct: 351 GDSFPGGSITGAPKIRAMQIIDELEPARRALYCGSLLYVDVRGEMDSSIAIRSLLIKDGQ 410 Query: 423 MHVQAGAGIVADSVPEREYEECWNKARALLKAVE 456 + G +VADS + EYEE K R L++ ++ Sbjct: 411 VSCWGGGAVVADSQWQAEYEESIAKVRVLMQTLQ 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: 515 Number of extensions: 31 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: 446 Length adjustment: 33 Effective length of query: 429 Effective length of database: 413 Effective search space: 177177 Effective search space used: 177177 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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