Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate Pf6N2E2_5665 Succinylornithine transaminase (EC 2.6.1.81)
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5665 Length = 406 Score = 216 bits (551), Expect = 8e-61 Identities = 144/392 (36%), Positives = 207/392 (52%), Gaps = 34/392 (8%) Query: 30 RAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYIE 89 R S VWD GRE IDFAGGIAV GH HP ++ A+ EQ KL H V EP + Sbjct: 30 RGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVGALTEQANKLWHVS-NVFTNEPALR 88 Query: 90 LAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIAR-AATGRAG-----VIAFTGAYHGRT 143 LA ++ V F ++ SG+EA E A K+AR A R G +IA ++HGRT Sbjct: 89 LAHKL---VNATFAERAFFCNSGAEANEAAFKLARRVAFDRFGSEKYEIIAALNSFHGRT 145 Query: 144 MMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQDIAA 203 + T+ + G+ YS G G GI + +A+++ + A Sbjct: 146 LFTVNVGGQS-KYSDGFGPKITGITHV----------PYNDLAALKAAISDKT-----CA 189 Query: 204 IIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLGIVPD 263 +++EP+QGEGG ++++Q R LCD H LL+ DEVQTG GR+G FA G+VPD Sbjct: 190 VVLEPIQGEGGVLPAEQAYLQGARDLCDAHDALLVFDEVQTGMGRSGHLFAYMHYGVVPD 249 Query: 264 LTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEEKLLE 323 + T AKS+GGGFPI+ + + + G G TY G+P+ACA A AV+ V ++L Sbjct: 250 ILTSAKSLGGGFPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVIDVVNTPEVLG 309 Query: 324 RSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVVRARE 383 + + KA L +I K+ + VRGLG ++ L D K A+ I A + Sbjct: 310 GVKTKHAKFKARLEQIGEKYGLFTQVRGLGLLIGCVL---NDAWKGKAK---DIFNAAEQ 363 Query: 384 KGLILLSCGTYYNVIRFLMPVTIPDAQLEKGL 415 +GL++L G +VIRF + + DA +++GL Sbjct: 364 EGLMILQAGP--DVIRFAPSLVVEDADIDEGL 393 Lambda K H 0.319 0.137 0.393 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: 393 Number of extensions: 13 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: 426 Length of database: 406 Length adjustment: 31 Effective length of query: 395 Effective length of database: 375 Effective search space: 148125 Effective search space used: 148125 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 17 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