Align Alpha-aminoadipate--LysW ligase LysX; AAA--LysW ligase LysX; EC 6.3.2.43 (characterized)
to candidate 351002 BT1474 ribosomal protein S6 modification protein-related protein (NCBI ptt file)
Query= SwissProt::Q7SI95 (275 letters) >FitnessBrowser__Btheta:351002 Length = 488 Score = 56.2 bits (134), Expect = 1e-12 Identities = 65/254 (25%), Positives = 111/254 (43%), Gaps = 27/254 (10%) Query: 9 LIEEGKKLGYQVATIYSKDFVLFSNDFTIDNDTDLFIQRNVSHNRALI-TSFLVEQVGYP 67 L E KK+ V I D + ++ D LFI+ S N S L Q G Sbjct: 216 LSEVAKKMNIHVEMITEDDAMRL-----LEFDA-LFIRTTTSLNHYTFHLSQLAAQNGMV 269 Query: 68 VINDHTTLIRCENKIFTTYILARHNIPTPKTFIAFDKT-NAIE-YSKKLGYPVVIKPVEG 125 VI+D ++IRC NK++ + + IP PK+ + F N+ E S+++G P ++K +G Sbjct: 270 VIDDPLSIIRCTNKVYLKELFEKERIPAPKSTLIFQSNENSFEQISEQVGAPFILKIPDG 329 Query: 126 SWGRMVAKADNLDVLYSYLEYQ-EFSTQKYKDIYYIQEFVNKPNRDIRIFVI-GDETPVG 183 S+ + K N + L + LE E S + EF D R+ ++ G Sbjct: 330 SYSIGMKKVSNEEELKTSLELLFEKSAILLAQAFTPTEF------DWRVGLLNGVPLYAC 383 Query: 184 IYRVNENNW---------RTNTALGAKAYPLKIDEELRELALKVKDIIGGFFLGIDIFED 234 Y + + +W R+ L ++ + + A+K ++IG G+D+ Sbjct: 384 KYYMAKGHWQIYCHYDSGRSRCGLVDTIPIYQVPRVVLDTAIKAANLIGKGLYGVDLKMV 443 Query: 235 KDRGYLVDEVNGVP 248 D+ Y++ E+N P Sbjct: 444 DDKAYVI-EINDNP 456 Lambda K H 0.320 0.139 0.411 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: 300 Number of extensions: 12 Number of successful extensions: 3 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: 275 Length of database: 488 Length adjustment: 30 Effective length of query: 245 Effective length of database: 458 Effective search space: 112210 Effective search space used: 112210 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: 49 (23.5 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