Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate Pf1N1B4_3440 Succinylornithine transaminase (EC 2.6.1.81)
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3440 Length = 406 Score = 221 bits (563), Expect = 3e-62 Identities = 143/392 (36%), Positives = 206/392 (52%), Gaps = 34/392 (8%) Query: 30 RAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYIE 89 R S VWD GRE IDFAGGIAV GH HP ++AA+ EQ KL H V EP + Sbjct: 30 RGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHVS-NVFTNEPALR 88 Query: 90 LAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARAA------TGRAGVIAFTGAYHGRT 143 LA ++ V F ++ SG+EA E A K+AR T + ++A ++HGRT Sbjct: 89 LAHKL---VDATFAERVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNSFHGRT 145 Query: 144 MMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQDIAA 203 + T+ + G+ YS G G GI + +A+++ A A Sbjct: 146 LFTVNVGGQS-KYSDGFGPKITGITHV----------PYNDLAALKA-----AVSDKTCA 189 Query: 204 IIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLGIVPD 263 +++EP+QGEGG S++Q R LCD H LL+ DEVQTG GR+G FA + G+ PD Sbjct: 190 VVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYGVTPD 249 Query: 264 LTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEEKLLE 323 + T AKS+GGGFPI+ + ++ + G G TY G+P+ACA A AV+ V ++L Sbjct: 250 ILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLN 309 Query: 324 RSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVVRARE 383 A ++ K L +I K+ + +VRGLG ++ L D K A+ I A Sbjct: 310 GVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVL---SDAWKGKAK---DIFNAAER 363 Query: 384 KGLILLSCGTYYNVIRFLMPVTIPDAQLEKGL 415 +GL++L G +VIRF + + DA ++ GL Sbjct: 364 EGLMILQAGP--DVIRFAPSLVVEDADIDAGL 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: 388 Number of extensions: 14 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: 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