Align Glutamate--LysW ligase ArgX; EC 6.3.2.- (characterized)
to candidate 7025111 Shewana3_2274 SSU ribosomal protein S6P modification protein (RefSeq)
Query= SwissProt::Q970U6 (282 letters) >FitnessBrowser__ANA3:7025111 Length = 299 Score = 89.4 bits (220), Expect = 9e-23 Identities = 74/239 (30%), Positives = 119/239 (49%), Gaps = 12/239 (5%) Query: 50 AIIRPVSMYRALYSSAVL---EAAGVHTINSSDVINVCGDKILTYSKLYREGIPIPDSII 106 A+I + Y SAVL E GV+ +N S I+ DK+ + + R GI +P + Sbjct: 60 AVIPRIGASITFYGSAVLRQFEMMGVYALNDSVGISRSRDKLRSMQLMSRRGIGLPITGF 119 Query: 107 ALSAEAALKAYEQ-RGFPLIDKPPIGSWGRLVSLIRDVFEGKTIIEHRELMGNSALKAHI 165 A + G PL+ K G+ G V L +++IE MG LKA+I Sbjct: 120 ANKPSDIPDLIDMVGGAPLVIKLLEGTQGIGVVLAETRKAAESVIE--AFMG---LKANI 174 Query: 166 -VQEYI-QYKGRDIRCIAIGEELLGCYARNIPPNEWRANVALGGTPSNIEVDEKLKETVV 223 VQEYI + G DIRC +G++++ R P E+R+N+ GGT S +++ + + + Sbjct: 175 MVQEYIKEANGADIRCFVLGDKVIAAMKRQAMPGEFRSNLHRGGTASLVKLTPEERSVAI 234 Query: 224 KAVSIVHGEFVSIDILEHPNKGYVVNELNDVPEFKGFMVATNINVAQKLVEYIKENYSK 282 +A + +D+L N G VV E+N P +G AT +VA ++E++++N K Sbjct: 235 RAAKTMGLNVAGVDLL-RSNHGPVVMEVNSSPGLEGIEGATAKDVAGAIIEFVEKNALK 292 Lambda K H 0.319 0.137 0.392 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: 194 Number of extensions: 12 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: 282 Length of database: 299 Length adjustment: 26 Effective length of query: 256 Effective length of database: 273 Effective search space: 69888 Effective search space used: 69888 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: 48 (23.1 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