Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_108401693.1 B9Z44_RS03080 aspartate aminotransferase family protein
Query= reanno::Putida:PP_4108 (416 letters) >NCBI__GCF_003063475.1:WP_108401693.1 Length = 398 Score = 174 bits (442), Expect = 3e-48 Identities = 132/406 (32%), Positives = 200/406 (49%), Gaps = 49/406 (12%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74 P+ L+HGR VWDT+GK Y+D + GI V LGH +P + A+Q Q ++ H + Sbjct: 18 PVALTHGRGLRVWDTNGKAYLDALAGIAVNTLGHAHPQLTPALQDQVGKMIHSC-----N 72 Query: 75 GPYLALMEQLS-QFVPVSYPLAGMLTNSGAEAAENALKVARG-----ATGKRAIIAFDGG 128 ++ L E L+ + V +S NSG EA E A+K+AR K I+ ++ Sbjct: 73 YYHIPLQEALAAKLVELSGMTNAFFCNSGLEANEAAIKLARKFGHMKGIEKPEIVVYEKA 132 Query: 129 FHGRTLATLNLNGKVAPYKQRVGELPGPVY--HLPYPSADTGVTCEQALKAMDRLFSVEL 186 FHGR+LATL G +++ E GP+ ++ P V +ALK Sbjct: 133 FHGRSLATLAATGN-----EKIKEGFGPMMEGYIRVP-----VNNIEALKKATE------ 176 Query: 187 AVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFP 246 +VAA FE +QGEGG ++ + Q +R+ CD+R L++IDE+Q G GRTG+ FA Sbjct: 177 GNPNVAAVFFETIQGEGGVKPMNTDYLQQVRQLCDKRDWLLMIDEVQCGMGRTGKWFAHQ 236 Query: 247 RLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQM 306 GI PD++ LAK + G+P+GAVV + G G T+ GNP++ A + ++ M Sbjct: 237 WSGIVPDVMPLAKGLGSGVPVGAVVAGPKAAHIFQPGNHGTTFGGNPLAMRAGVETIRIM 296 Query: 307 TD----ENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPA 362 + +N+ G A+ + K + + G G M GI+ G Sbjct: 297 EEDKLLDNVLKVGAHLHAALHRELDGVKG------VKEIRGQGLMIGIDLDRPCG----- 345 Query: 363 QLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDIL 408 +M+ A GLLL S A ++RL+ PL I +E + IL Sbjct: 346 ---VLMQRALDAGLLL--SVTADSVVRLVPPLIITEAEADEVVAIL 386 Lambda K H 0.320 0.137 0.402 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: 432 Number of extensions: 17 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: 416 Length of database: 398 Length adjustment: 31 Effective length of query: 385 Effective length of database: 367 Effective search space: 141295 Effective search space used: 141295 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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