Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_040304857.1 CMTB2_RS01800 aminodeoxychorismate synthase component I
Query= curated2:Q58475 (474 letters) >NCBI__GCF_000170735.1:WP_040304857.1 Length = 316 Score = 92.4 bits (228), Expect = 2e-23 Identities = 94/296 (31%), Positives = 143/296 (48%), Gaps = 42/296 (14%) Query: 181 NNDNKEEKTTENKDLKIKSNMSKEEFIEAVKKAKEYIFAGDIFQVVLSRRIEIDLDNLDH 240 N K K T+ K K K+ F E +++ K G+ + + L+ + +I+L N D Sbjct: 42 NYKKKRCKITKISPPKFKDY--KKAFFEVIEEIKN----GNTYLLNLTFQSKIEL-NCDL 94 Query: 241 LKIYKKVREINPSPYMYYLDFGDRKIIGSSPEILVRTDYKDNKRLVITRPIAGTIRRGKT 300 + ++ N S ++ L F D K + SPE V+ K+NK + T P+ GTI T Sbjct: 95 IDVF------NNSNALFKLYFKD-KFVCFSPERFVKI--KNNK--IYTYPMKGTI--DAT 141 Query: 301 EEEDKELEKKLLSDEKERAEHVMLVDLARNDIGKISKFGTVEVTDFMIIEKYS----HVQ 356 KE K+LS+ KE AEH M+VDL RND+G I + V+V F I+K + Sbjct: 142 IPNSKE---KILSNIKEMAEHTMVVDLLRNDLGIIGR--DVKVNKFRYIDKIKAQNKEIL 196 Query: 357 HIVSNVVGELKDNYDS--FLAVKATFPAGTLSGAPKVRAMEIIEELEKTWRGPYGGGVGY 414 + S + L N++ +K PAG++SG PK + +EII+ +E RG Y G G Sbjct: 197 QVSSEIEATLPKNWNKNYINLIKKMLPAGSISGTPKKKTVEIIKRVENYKRGFYTGIFGI 256 Query: 415 FGWDDLMDLAITIRTFVISKNKGY---------IQVGAGIVADSIPENEWEETERK 461 +D A+ IR I K K + + G GI DS + E++E +K Sbjct: 257 TDEKTFLDSAVIIR--YIEKPKQFSTFHFPFYIYKSGGGITIDSNLKEEYKELIQK 310 Lambda K H 0.317 0.139 0.393 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: 399 Number of extensions: 24 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: 474 Length of database: 316 Length adjustment: 30 Effective length of query: 444 Effective length of database: 286 Effective search space: 126984 Effective search space used: 126984 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 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