Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_007473232.1 CMTB2_RS01220 glutamate-1-semialdehyde-2,1-aminomutase
Query= SwissProt::Q88FI7 (416 letters) >NCBI__GCF_000170735.1:WP_007473232.1 Length = 420 Score = 130 bits (326), Expect = 1e-34 Identities = 96/319 (30%), Positives = 153/319 (47%), Gaps = 36/319 (11%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNP----AVVEAIQAQATRLTHYAFN 70 P + G A ++D +G +Y+D++ G L GHC+ A++EA++ Sbjct: 29 PPFIEKGEGAYIFDIEGNKYLDYIQSWGPLIFGHCDKDTQNAIIEAVK-----------K 77 Query: 71 AAPHGPYLALMEQLSQFVPVSYPLAGML--TNSGAEAAENALKVARGATGKRAIIAFDGG 128 G + +L++ V +P ++ NSG EA +A+++ARG TGK II F+G Sbjct: 78 GVSFGAPTKVEVELAKEVLELFPHLNLIRFVNSGTEATMSAIRLARGYTGKDDIIKFEGC 137 Query: 129 FHGRTLATLNLNGKVAPYKQRVGELPGPVYHLP-YPSADTGVTCEQALKAMDRLFSVELA 187 +HG + + L G A + +P P T L + + SV+ Sbjct: 138 YHGHSDSLLVSAGSGA-----------ATFGVPSSPGVPADFTKHTLLAKYNDIESVKKC 186 Query: 188 VE--DVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAF 245 E DV I EP+ G + + F LR C+ G ++I DE+ SGF R R +F Sbjct: 187 FENGDVGCVIIEPIAGNMSLVPGEKEFLGELREICNHYGAVLIFDEVMSGF-RASLRGSF 245 Query: 246 PRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGG---LGGTYSGNPISCAAALAS 302 GI+ D++ K I GGMP+GA G+KE+M L G GT SGNP++ +A L Sbjct: 246 DIYGIKADIVTFGKVIGGGMPVGAFAGKKEIMEKLSPVGPVYQAGTLSGNPVAMSAGLTV 305 Query: 303 LAQMTDENLATWGERQEQA 321 + ++ EN + E +++A Sbjct: 306 IKKL-KENPEIYKELEDKA 323 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: 409 Number of extensions: 19 Number of successful extensions: 5 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: 420 Length adjustment: 32 Effective length of query: 384 Effective length of database: 388 Effective search space: 148992 Effective search space used: 148992 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 Apr 10 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