Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate CCNA_03048 CCNA_03048 para-aminobenzoate synthetase component I
Query= curated2:Q9Z4W7 (511 letters) >FitnessBrowser__Caulo:CCNA_03048 Length = 524 Score = 243 bits (619), Expect = 2e-68 Identities = 167/429 (38%), Positives = 233/429 (54%), Gaps = 30/429 (6%) Query: 87 VSGGVARYSYVGHRPVPL----EPTGGDPLTALRSHLARSVAPVPGLPPFHGGVVGYLGY 142 V+GG R+SY+ P + DP AL + + + P PPF GGVVG Y Sbjct: 113 VTGGAGRWSYLLRAPDATMSLSDKDPADPFAALAALVGPRLPSHPEGPPFQGGVVGLGAY 172 Query: 143 EAARHFEDLPLAAGPPPGLPESAFLAADDLVVFDHATRRVLLMTLYRPARESYDDAVARI 202 E EDL L+ P L + + A L+ FDH R+V+ + E+ A + Sbjct: 173 ELGDRVEDLGLSRTDWPDLTCARYPA---LLAFDHHARQVIAVGRGEAEAEANARAADAL 229 Query: 203 VRLNRALRRAPAPAAFSGRPLAAATPADHGTQGWTANLTEAQFTERVARAREHIAAGDAF 262 L A PA L A+ PA + T VA+ I G+ F Sbjct: 230 AWLEVAAPERAEPAGPLCADLVASDPATYETA--------------VAQVVARIVGGEIF 275 Query: 263 QIVLSRRLSRPLRAR--PTDLYRHLRATNPSPYMYHLSLGGGRHVIGASPELLVKAEGR- 319 Q ++R + L A P DL+ LRA +P+P+ + L G R ++ SPE +K + Sbjct: 276 QANIARAWTGRLAAGVDPFDLFVRLRAQSPAPFSAYWRLPG-RALVSNSPERFLKLDAAG 334 Query: 320 TVRTRPLAGTRPRHPDPAEDLRLERELRADEKERAEHVMLVDLGRNDLGRVTEPGTVRVE 379 ++T+P+ GTRPR DP ED L EL A +K+RAE++M+VDL RNDL RV+ G+VR Sbjct: 335 AIQTQPIKGTRPRGRDPVEDRALAAELLASDKDRAENLMIVDLMRNDLARVSPAGSVRAP 394 Query: 380 RLMRVERFSHVMHLSSTVRGRLAEGRDALDALRSAFPAGTLSGAPKIRAMEIIAELEPEQ 439 L +VE F++V HL STV RLA GR D LR++FP G+++GAPK++AM++IAELEP Sbjct: 395 ELFKVESFANVHHLVSTVTARLAPGRGVADLLRASFPPGSITGAPKVQAMKVIAELEP-P 453 Query: 440 RGVYGGALGFVGADGLTDFAIALRTM-VVADG---HVHVQAGAGIVADSDPAAEFRETLH 495 RG Y G+L + G DG D ++ +RT+ +V DG + +AGAGIVADSDP E ET Sbjct: 454 RGPYCGSLFWAGVDGAFDSSVLIRTVGLVQDGAGWRLEARAGAGIVADSDPRGERLETEA 513 Query: 496 KSRAMLTAV 504 K A+ TA+ Sbjct: 514 KIAALKTAL 522 Score = 25.0 bits (53), Expect = 0.007 Identities = 17/52 (32%), Positives = 21/52 (40%), Gaps = 9/52 (17%) Query: 135 GVVGYLGYEAARHFEDLPLAAGPPPGLPESAFLAADDLVVFDHATRRVLLMT 186 GV G +ARH PPP P L + + HA R V L+T Sbjct: 48 GVPSGSGTVSARH---------PPPNRPRGLALVSVRRARYHHAMRHVALLT 90 Lambda K H 0.319 0.134 0.394 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: 723 Number of extensions: 40 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 511 Length of database: 524 Length adjustment: 35 Effective length of query: 476 Effective length of database: 489 Effective search space: 232764 Effective search space used: 232764 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 (21.8 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