Align Anthranilate synthase component 1 1; EC 4.1.3.27; Anthranilate synthase component I 1 (uncharacterized)
to candidate WP_092485907.1 BM299_RS14595 aminodeoxychorismate synthase, component I
Query= curated2:Q5V448 (489 letters) >NCBI__GCF_900115975.1:WP_092485907.1 Length = 476 Score = 313 bits (801), Expect = 1e-89 Identities = 176/399 (44%), Positives = 238/399 (59%), Gaps = 8/399 (2%) Query: 77 AGGTLAALTEFLDGERLVRGDCDVPYPCGAVGWLSYDVARELESLPDSADADRALPNLQV 136 +G +A L + L + + P+ GAVG+ SYD+ R E +P+ A D P++ + Sbjct: 75 SGSPMAELKKLLARYAMPPENGLFPFNGGAVGYFSYDLGRLFEKIPEQALDDLGTPDIWL 134 Query: 137 ARYDRFAAWEEPRGESVTLRVTACPRVDDFETPELAYEFGKQHALDLARAAAQGDPSVED 196 YD A + R T+ T P E + A E + ++ Q P E Sbjct: 135 GFYDTVVA-VDVRTNEATVISTGLP-----ERGDAALERANRRLREVEELLRQDSPRSER 188 Query: 197 PPVETDEAT--FESDCTRESFADRVQTVKQYIRDGDTFQANVSQRLRAPAAVHPVEAFDA 254 + E + S+ T E + + V+ +YI GD FQ N++QR P V E + Sbjct: 189 KNIRWLEGSPPLTSNFTPEEYRNMVKRAIEYIAAGDIFQVNLTQRFSVPQRVKAWELYKK 248 Query: 255 LRTVNPAPYSALLEFPGVDLVSASPELLLHRDGDRIETEPIAGTRPRGETPDADDRLETD 314 LRT+NPAP++A L G++++SASPE L GDR+ET PI GTRPRG TP+ DDRL + Sbjct: 249 LRTINPAPFAAFLSCDGMEILSASPERFLKVVGDRVETCPIKGTRPRGRTPEEDDRLRRE 308 Query: 315 LLDDEKERAEHAMLVDLERNDLGKVSKFGSVEVSDYRRVDRYSEVMHLVSVVEGRLRDGA 374 L + EK+RAE M+VDLERNDLG+V + GSV+V + R+++Y+ V HLVS VEGRL G Sbjct: 309 LWESEKDRAELMMIVDLERNDLGRVCEIGSVKVPELFRLEKYATVFHLVSTVEGRLLPGK 368 Query: 375 SLQDAIAAVFPGGTITGAPKPRTMEIIDEVEATRRGPYTGSIGLFGFDGRATLNIVIRTL 434 + D +AA FPGG+ITGAPK R MEII+E+E RRG YTGSIG GFDGR LNIVIRT+ Sbjct: 369 DITDLLAASFPGGSITGAPKIRAMEIIEEMEPVRRGVYTGSIGYIGFDGRVDLNIVIRTI 428 Query: 435 VRYAEEYHLRVGAGVVHDSDPDREYQETLDKGRALVNAV 473 + + +VG G+ DSDP +EY ETLDK RAL A+ Sbjct: 429 LAAGGNMYFQVGGGITADSDPHKEYVETLDKARALARAL 467 Lambda K H 0.317 0.135 0.396 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: 616 Number of extensions: 22 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: 489 Length of database: 476 Length adjustment: 34 Effective length of query: 455 Effective length of database: 442 Effective search space: 201110 Effective search space used: 201110 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: 52 (24.6 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