Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate CA265_RS14515 CA265_RS14515 aminodeoxychorismate synthase component I
Query= curated2:Q08653 (461 letters) >FitnessBrowser__Pedo557:CA265_RS14515 Length = 418 Score = 184 bits (466), Expect = 6e-51 Identities = 124/367 (33%), Positives = 187/367 (50%), Gaps = 19/367 (5%) Query: 95 DELPSF----RGGAVGFVSYDYISYIEKVKVKASV---FPTFYFVVPEHLIIFDHLKNNV 147 D+L SF + GF YD + IE + S FP YF VP++LI F V Sbjct: 60 DQLKSFYALHKQWIFGFFGYDLKNEIEDLHSNNSDHLNFPDLYFFVPKYLIAFKKGNAEV 119 Query: 148 FIISDSPEELTSKVLSPFEEKPEKNVFVTEPESNFEREQFYKVVEKAKKYIVEGDIFQVV 207 I PE + +++ S F+ K E + ++Q+ + VE + +I+ GDI++V Sbjct: 120 LI---GPESILAEIDS-FQLKTEIQSKKAKVAQRLSKDQYVQKVEALRDHIIRGDIYEVN 175 Query: 208 LSQAFTFKTT-LDPFYIYRALRMINPSPYMFYLKFGDTVVLGSSPETMAKVEGDKATVKP 266 Q F + +DP + AL ++P+P+ Y K +L ++PE G K T +P Sbjct: 176 FCQEFFAENAEIDPVQTFEALNSVSPTPFAGYFKVQGNYILSATPERFLCKRGSKLTSQP 235 Query: 267 IAGTRPRGRTVEEDLKLERELLNDEKEIAEHVMLVDLGRNDLGRVCKEGTVRVEKKMVIE 326 I GT R ED ++ +L ND KE AE+VM+VDL R+DL + +G+V V++ I Sbjct: 236 IKGTAKRSLDPMEDEAIKLQLRNDIKEQAENVMIVDLVRHDLTKSAVKGSVTVDELFGIY 295 Query: 327 RYSHVMHIVSQVSGELKDDKDAVDVFEATFPAGTVSGAPKVRAMEIIEELEPTPRGPYAG 386 + V ++S +S EL +D + FP G+++GAPKV+AM++IEE E T RG Y+G Sbjct: 296 SFPQVHQMISTISCELNPAIHFIDAIKNAFPMGSMTGAPKVKAMKLIEEYEVTKRGIYSG 355 Query: 387 AVGYFSFPDDKGRMNMDSAITIRSFFFKGKQGWL--QAGAGIVYDSVPEREYQETLNKLR 444 + G S D D + IRS + +L Q G I Y S EY+E L K Sbjct: 356 SFGCISAAGD-----FDFNVVIRSILYNAASNYLSFQVGGAITYQSNAVLEYEECLLKAS 410 Query: 445 ALFRSLE 451 A+ + LE Sbjct: 411 AILKVLE 417 Lambda K H 0.319 0.137 0.392 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: 467 Number of extensions: 20 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: 461 Length of database: 418 Length adjustment: 32 Effective length of query: 429 Effective length of database: 386 Effective search space: 165594 Effective search space used: 165594 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 (21.7 bits) S2: 51 (24.3 bits)
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