Align Anthranilate synthase component 1 1; EC 4.1.3.27; Anthranilate synthase component I 1 (uncharacterized)
to candidate WP_051242775.1 H537_RS43555 aminodeoxychorismate synthase, component I
Query= curated2:Q5V448 (489 letters) >NCBI__GCF_000430725.1:WP_051242775.1 Length = 412 Score = 184 bits (468), Expect = 4e-51 Identities = 106/270 (39%), Positives = 153/270 (56%), Gaps = 11/270 (4%) Query: 211 TRESFADRVQTVKQYIRDGDTFQANVSQRLRAPAAVHPVEAFDALRTVNPAPYSALLEFP 270 +R+ FAD + + IRDG+T+Q N + R+R + HPV + LRT P Y A + P Sbjct: 122 SRQDFADAIDGIHAAIRDGETYQINYTYRVRGRSWGHPVALYRRLRTRQPVSYGAFVSLP 181 Query: 271 -GVDLVSASPELLLHRDGDRIETEPIAGTRPRGETPDADDRLETDLLDDEKERAEHAMLV 329 G ++S SPEL L I +P+ GT PR + +AD + L +D K RAE+ M+V Sbjct: 182 EGGAVLSCSPELFLRHQSGLITAKPMKGTAPRLQVAEADSVMARWLSEDTKNRAENLMIV 241 Query: 330 DLERNDLGKVSKFGSVEVSDYRRVDRYSEVMHLVSVVEGRLRDGASLQDAIAAVFPGGTI 389 DL RNDLG++++ GSV V ++ + V + S V+ ++ G L + + A FP G+I Sbjct: 242 DLLRNDLGRIARIGSVRVPQLFGIESHPTVFQMTSTVQAQIAPGVGLPELLRATFPCGSI 301 Query: 390 TGAPKPRTMEIIDEVEATRRGPYTGSIGLFGFDGRAT-----LNIVIRTLVRYA-----E 439 TGAPK RTME+I E+E+T RG YTGSIG + T L++ IRT + A Sbjct: 302 TGAPKKRTMELIAELESTPRGLYTGSIGWLDLEPGQTCPDLCLSVAIRTSLLSAPLHDIA 361 Query: 440 EYHLRVGAGVVHDSDPDREYQETLDKGRAL 469 + +GAG+ DS D E++E KGR L Sbjct: 362 SVEMGLGAGITLDSQADAEFEECRLKGRFL 391 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: 492 Number of extensions: 21 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: 489 Length of database: 412 Length adjustment: 33 Effective length of query: 456 Effective length of database: 379 Effective search space: 172824 Effective search space used: 172824 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: 51 (24.3 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