Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_019895717.1 A377_RS0107825 hypothetical protein
Query= curated2:Q9XAZ0 (491 letters) >NCBI__GCF_000384235.1:WP_019895717.1 Length = 485 Score = 252 bits (643), Expect = 2e-71 Identities = 153/375 (40%), Positives = 221/375 (58%), Gaps = 24/375 (6%) Query: 111 SLPRFTGGLVGYFGYETIYNFEHFAHRLKNTTKADPLGTPDILLMLSQELAVIDNLSGKI 170 SLP FTGG YFGYE FA L+ + P + +ID+ +G Sbjct: 125 SLP-FTGGWFVYFGYE-------FAQVLEPSLSLPASNLPLAKWVRIPSAILIDHQTGHG 176 Query: 171 HLVVYADPSQPDGYERARERLEDIRTQLRQSCAIPLSLGSKHTEAVSEFGEEP---FKAC 227 +LV ++P R +D++ R ++P AV+E ++P F Sbjct: 177 YLV-----AEPGFEHRLHTLYQDLQQVGRVETSVP-------EIAVAEIHQDPPQRFTQG 224 Query: 228 VNKIKDYIFAGDCMQVVPSQRMSMEFTDSPLA-LYRALRTLNPSPYLFYYDFGDFHIVGS 286 V++IKDYI AGD QV S++ ++ ++ +YRALR NP+P+ Y DFGD+ ++ S Sbjct: 225 VDRIKDYILAGDVFQVNLSRQWEVDVKNASAPNVYRALRQANPAPFAAYADFGDWQVLSS 284 Query: 287 SPEILVRRERDDVIVRPIAGTRLRGKTPAEDLANEQDLLSDAKEIAEHVMLIDLGRNDVG 346 SPE LV + + V RPIAGTR R +DLA ++L + KE+AEH+MLIDL RND+G Sbjct: 285 SPERLVTSDGEHVATRPIAGTRRRSSDTEKDLALIRELQAHPKEVAEHIMLIDLERNDLG 344 Query: 347 RISKTGEVKVTDKMVIEKYSHVMHIVSNVEGRLKDGMTNMDILAATFPAGTLSGAPKVRA 406 R+S+ G V V + M IE Y +V HIVSN++GRL+ G + +DI AATFP GT++G PK+R Sbjct: 345 RLSQPGSVAVDELMAIETYQYVHHIVSNIQGRLQPGTSPLDIFAATFPGGTITGCPKIRC 404 Query: 407 MEIIEEVEPSKRGIYGGAVGVWGFNNDMDLAIAIRTAVVKNNTLYVQSGAGVVADSDPAS 466 MEII E+E + R Y G++G + +D I IRT V + L ++GAG+VADSDP Sbjct: 405 MEIIAELEQTPREAYTGSLGYINRDGRLDSNILIRTFVQQGERLRFRAGAGIVADSDPEK 464 Query: 467 EWQETQNKARAVIRA 481 E ET++KA+ +++A Sbjct: 465 ELAETRHKAKGLLKA 479 Lambda K H 0.318 0.136 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: 630 Number of extensions: 35 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 491 Length of database: 485 Length adjustment: 34 Effective length of query: 457 Effective length of database: 451 Effective search space: 206107 Effective search space used: 206107 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: 52 (24.6 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