Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate 8502295 DvMF_3003 putative transcriptional regulator, GntR family (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >FitnessBrowser__Miya:8502295 Length = 394 Score = 330 bits (845), Expect = 6e-95 Identities = 190/391 (48%), Positives = 244/391 (62%), Gaps = 9/391 (2%) Query: 14 LARRAERMNPSVIREILKVTEKPGIISLAGGLPSPKTFPVSAFAAASAAVLANDGPAALQ 73 LA+R E + S IREILKVT +P IIS AGGLP P +FPV A A+A+A+VL GP ALQ Sbjct: 3 LAQRMESVPRSYIREILKVTAQPDIISFAGGLPHPASFPVDAVASAAASVLEEAGPEALQ 62 Query: 74 YAASEGYAPLRQAIADFLPW---DVDADQILITTGSQQALDLIAKVLIDENSRVLVETPT 130 Y +EG+ PLRQ IAD +V D ILITTGSQQALDL+AK ID RV++E P Sbjct: 63 YTTTEGFPPLRQWIADRYKRQGINVSPDDILITTGSQQALDLVAKACIDRGGRVVMERPG 122 Query: 131 YLGALQAFTPMEPSVVAVASDDEGVLIDDLKAKVGTGADKARFLYVLPNFQNPTGRTMTE 190 YLGA+Q F+ P V V GV D L+ K TGA + Y +P+FQNP+G T E Sbjct: 123 YLGAIQCFSVFGPDFVTVPLTPRGVDTDALR-KAATGA---QVFYAVPSFQNPSGITYDE 178 Query: 191 ARRAALVKAAAELNLPLVEDNPYGDLWFDNPPPAPLTARNPEGCIYMGSFSKVLAPGLRL 250 R + + AE +VEDNPYG+L F P+ A + +GSFSKV++PGLRL Sbjct: 179 QTRREVAEIMAETGCLMVEDNPYGELRFMGQHLPPVRAYMQAPSVLLGSFSKVVSPGLRL 238 Query: 251 GFVVAPKAVYPKLLQAKQAADLHTPGYNQRLVAEVMKGNFLDRHVPTIRALYKQQCEAML 310 G+V AP+ V ++ AKQA+DLHTPG+ QR++ + N +D+H+ +IRA Y Q +AM+ Sbjct: 239 GWVCAPQEVLNPMITAKQASDLHTPGFTQRILHRYLMDNDVDKHIASIRARYGAQRDAMV 298 Query: 311 AALTQEMAGLGVEWNRPDGGMFLWVRLPEGMSAIELLPQAVERNVAFVPGAAFYADNADP 370 A+ + V P+GGMFLW LPEG+SA L +A+ER VAFVPG FY D D Sbjct: 299 QAIRRHFPE-DVACTEPEGGMFLWCTLPEGISAEALFHKAIERKVAFVPGRPFYVDETDD 357 Query: 371 RTLRLSFVTSTVEQIATGIAALAAAIRSHKG 401 T RL+F S+ E I GIA L +R + G Sbjct: 358 -TFRLNFSNSSPELIEEGIARLGQCLREYLG 387 Lambda K H 0.318 0.134 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: 463 Number of extensions: 21 Number of successful extensions: 4 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: 401 Length of database: 394 Length adjustment: 31 Effective length of query: 370 Effective length of database: 363 Effective search space: 134310 Effective search space used: 134310 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 (21.7 bits) S2: 50 (23.9 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