Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_013259975.1 DEBA_RS15920 aminodeoxychorismate synthase, component I
Query= curated2:P95646 (500 letters) >NCBI__GCF_000143965.1:WP_013259975.1 Length = 754 Score = 283 bits (723), Expect = 2e-80 Identities = 184/465 (39%), Positives = 251/465 (53%), Gaps = 21/465 (4%) Query: 23 LTADLDTPVSLMLKLAE--ARTDTFMLESVTGGEIR-GRYSVVGMKPDLIWQCHGQDSRI 79 LT L+ P ++ A A T +L+S GGE+ R+ ++G++P L + G+ ++ Sbjct: 16 LTKPLERPEPVLDVAARFAAEPGTVLLQS--GGELDCARHHILGLRPWLTLR--GRADQM 71 Query: 80 NREARFDRQAFQPLEGHPLETLRALIAESRIEMPADLPPIAAGLFGYLGYDMIRLVEHLP 139 N D Q+ + L P + LRAL+ ++ PAD P+ AGL GYL YD+ +E LP Sbjct: 72 N--LTIDGQSHE-LGVEPFDLLRALVDHFQLAPPADDAPLRAGLLGYLAYDLKDRLERLP 128 Query: 140 GINPDPLGLPDAVLMRPSVVAVLDGVKGEVTVVAPAWVSSGLSARAAYAQAAERVMDAL- 198 + D LP L+ PSV+ V D K +AP W R Q A +D Sbjct: 129 RTSVDDQNLPHIHLIAPSVLVVFDRPKNRAVALAP-WRD-----RPGGRQEARAALDGFF 182 Query: 199 RDLDRAPPAQRDFGEVAQVGEMRSNFTHEGYKAAVEKAKDYIRAGDIFQVVPSQRWAQDF 258 R L PPA F G R+NF Y AAVE+ + YI AGD++QV SQR+ DF Sbjct: 183 RALQGPPPAPGAFAR----GPWRANFARGPYMAAVERIRQYIAAGDVYQVNMSQRFEADF 238 Query: 259 RLPPFALYRSLRKTNPSPFMFFFNFGGFQVVGASPEILVRLRDREVTVRPIAGTRKRGAT 318 FAL+R+L NP+PF F N G Q+V SPE + R V RPI GTR R A Sbjct: 239 SGDAFALHRALHAANPAPFFAFVNAGDHQIVCTSPERFLLQRGDWVETRPIKGTRPRLAD 298 Query: 319 PEEDRALEADLLSDKKELAEHLMLLDLGRNDVGRVAKIGTVRPTEKFIIERYSHVMHIVS 378 P +D A+ +L K+ AE M++DL RND+GR +VR +E + +V H+VS Sbjct: 299 PAQDEAMGRELQESPKDAAELSMIVDLLRNDLGRSCAAQSVRVLAHKRLEAWRNVYHLVS 358 Query: 379 NVVGEIAEGEDALSALLAGLPAGTVSGAPKVRAMEIIDELEPEKRGVYGGGVGYFAANGE 438 V G +A G+ + L P G+++G PK+RAMEIIDELEP +R +Y G +GY + Sbjct: 359 LVEGRLAPGKRGVDLLEGCFPGGSITGCPKIRAMEIIDELEPNRRHIYTGSIGYIGFDQT 418 Query: 439 MDFCIALRTAVLKDETLYIQSGGGVVYDSDPEAEYQETVNKARAL 483 MD IA+RT + GGGVVYDSDP AEY ET++K R L Sbjct: 419 MDLNIAIRTVTIAHGRASFGVGGGVVYDSDPAAEYDETLHKGRTL 463 Lambda K H 0.320 0.137 0.400 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: 836 Number of extensions: 45 Number of successful extensions: 2 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: 500 Length of database: 754 Length adjustment: 37 Effective length of query: 463 Effective length of database: 717 Effective search space: 331971 Effective search space used: 331971 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: 53 (25.0 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