Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_090438593.1 BLS63_RS01095 aspartate aminotransferase family protein
Query= reanno::Putida:PP_4108 (416 letters) >NCBI__GCF_900100495.1:WP_090438593.1 Length = 416 Score = 629 bits (1622), Expect = 0.0 Identities = 311/415 (74%), Positives = 355/415 (85%) Query: 1 MNQESISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQ 60 M+ SIS S+AIVHPI+LSHGRNAEVWD+ GKRYIDFVGGIGVLNLGHC+P +VEA++ Q Sbjct: 1 MSHASISNSLAIVHPISLSHGRNAEVWDSTGKRYIDFVGGIGVLNLGHCHPRIVEAVREQ 60 Query: 61 ATRLTHYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKR 120 A RLTH AFNA PH Y+ LME L++FVPVSYPL+GMLTNSGAEAAENALK R ATG+ Sbjct: 61 AGRLTHSAFNAVPHEGYVQLMEALARFVPVSYPLSGMLTNSGAEAAENALKSVRAATGRS 120 Query: 121 AIIAFDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDR 180 A+IAFDGGFHGRTLATLNLNGKVAPYKQ+VG LPGPVYHLPYPSAD GV+ EQAL AM+R Sbjct: 121 AVIAFDGGFHGRTLATLNLNGKVAPYKQKVGTLPGPVYHLPYPSADNGVSREQALAAMER 180 Query: 181 LFSVELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTG 240 LFSVE+ +VA FI EP+QGEGGF ALD AFAQ LR+FCD GI++IIDE+QSGFGR+G Sbjct: 181 LFSVEIDQAEVACFIVEPIQGEGGFQALDAAFAQDLRQFCDRHGIVLIIDEVQSGFGRSG 240 Query: 241 QRFAFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAAL 300 QRFAF RLGIEPDLLLL KSIAGG+PLGAVVGR+ELM ALP+GGLGGTYSGNP++CAAAL Sbjct: 241 QRFAFSRLGIEPDLLLLGKSIAGGLPLGAVVGRRELMDALPRGGLGGTYSGNPLACAAAL 300 Query: 301 ASLAQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPA 360 ASL +M+D NLATWGE Q I +RY+RW+ +P +GRLTGVGAMRGIE +ADG P Sbjct: 301 ASLTEMSDANLATWGELQAGTIEARYQRWQGEPWAPLLGRLTGVGAMRGIELRSADGGPG 360 Query: 361 PAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 +LA ++ +AR +GLLLMPSGKARHIIRLLAPLT E E LEEG DILE+CLA L Sbjct: 361 SERLAALLGSAREQGLLLMPSGKARHIIRLLAPLTCERERLEEGFDILERCLAGL 415 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: 669 Number of extensions: 21 Number of successful extensions: 1 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: 416 Length adjustment: 31 Effective length of query: 385 Effective length of database: 385 Effective search space: 148225 Effective search space used: 148225 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