Align anthranilate synthase component I (EC 4.1.3.27) (characterized)
to candidate WP_007472826.1 CMTB2_RS00185 anthranilate synthase component I family protein
Query= metacyc::MONOMER-281 (461 letters) >NCBI__GCF_000170735.1:WP_007472826.1 Length = 469 Score = 318 bits (815), Expect = 2e-91 Identities = 190/444 (42%), Positives = 268/444 (60%), Gaps = 28/444 (6%) Query: 29 EFAFLLESVELGSAFGRHSFIGIGKKDVLVFEKGILRTSNQQLDYTSS--PLKAIKDWLE 86 E FLLESV + ++ G +SFI IG+K+ + ++ + +++ S P +K + Sbjct: 27 EKLFLLESV-INNSDGNYSFIFIGEKEKIFYKDYKTHYFDGEIEQVLSEDPFTFLKKYYS 85 Query: 87 VYRYSVKHDELPS-----FRGGAVGFVSYDYISYIEKVKVKASV-------FPTFYFVVP 134 + K+ EL F G VG++ YD + E V K P FY + P Sbjct: 86 KIDFD-KYRELSKTLKIGFVDGFVGYIGYDMVKIFEPVLKKVMDNLKDEINIPDFYMIRP 144 Query: 135 EHLIIFDHLKNNV-FIISDSPEELTSKVL-----SPFEEKPEKNV-FVTEPESNFEREQF 187 + +I + H + + II+D E V+ S ++ P K + EP+ F +E+F Sbjct: 145 KIVIGYSHKFSELTIIINDKKYEKLLYVIRDLINSSYKHFPLKKAEIIEEPKFIFSKEKF 204 Query: 188 YKVVEKAKKYIVEGDIFQVVLSQAFTFKTTLDPFYIYRALRMINPSPYMFYLKFGDTVVL 247 +++V AK+ I GDIFQ+VLS K +D YR LR NPSPY+FYL D ++ Sbjct: 205 FEMVNNAKENIKNGDIFQIVLSNRLKVKAKVDRLSFYRKLRSKNPSPYLFYLDIDDFAII 264 Query: 248 GSSPETMAKVEGDKATVKPIAGTRPRGRTVEEDLKLERELLNDEKEIAEHVMLVDLGRND 307 GSSPE M ++ ++PIAGTR RG ++++DL+LE++++ND KE+AEH+MLVDLGRND Sbjct: 265 GSSPEVMVRLNDGMILLRPIAGTRKRGESLKKDLELEKDMINDPKEVAEHIMLVDLGRND 324 Query: 308 LGRVCKEGTVRVEKKMVIERYSHVMHIVSQVSGELKDDKDAVDVFEATFPAGTVSGAPKV 367 +GRV K G+V+V + M +ERYSHVMH+VS V G+L D D+F+ATF AGT++GAPK+ Sbjct: 325 VGRVAKAGSVKVPEIMRVERYSHVMHMVSDVVGKLDSKFDMFDLFKATFTAGTMTGAPKI 384 Query: 368 RAMEIIEELEPTPRGPYAGAVGYFSFPDDKGRMNMDSAITIRSFFFKGKQGWLQAGAGIV 427 +AME+I + E RG YAG+VGYF F NMDSAITIRS KG + QAGAGIV Sbjct: 385 KAMELIAKYEGIKRGYYAGSVGYFGFDG-----NMDSAITIRSALIKGDEVIFQAGAGIV 439 Query: 428 YDSVPEREYQETLNKLRALFRSLE 451 DS PE EY+E NKL AL +L+ Sbjct: 440 ADSKPELEYKEVNNKLGALVATLK 463 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: 608 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: 461 Length of database: 469 Length adjustment: 33 Effective length of query: 428 Effective length of database: 436 Effective search space: 186608 Effective search space used: 186608 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