Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate Synpcc7942_0943 Synpcc7942_0943 acetylornithine aminotransferase
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__SynE:Synpcc7942_0943 Length = 422 Score = 213 bits (541), Expect = 1e-59 Identities = 138/400 (34%), Positives = 211/400 (52%), Gaps = 30/400 (7%) Query: 25 PVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAY 84 P+ ER E VWD +GR Y+DF GIA GH HP+++ A+ +Q+ KL H L Y Sbjct: 35 PLALERGEGCRVWDTQGRSYLDFVAGIATCTLGHAHPELVDAISDQIRKLHHV--SNLYY 92 Query: 85 EPYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARA------ATGRAGVIAFTGA 138 P E + A + SG+EA E A+K+AR ++ + Sbjct: 93 IP--EQGQLAAWLTANSCADRVFFCNSGAEANEAAIKLARKHGNTVLEAENPIILTAQAS 150 Query: 139 YHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQP 198 +HGRT+ + TG+ + L+ G FR V +D A + + DA Sbjct: 151 FHGRTLAAVTATGQPKYHKGFQPLVQG--FRY--------VPYNDLAALEATLAELDAAG 200 Query: 199 QDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQL 258 + +AAI++EP+QGEGG +++ Q +R LCDQ +LLI DEVQ G GR+G + E L Sbjct: 201 ETVAAILLEPLQGEGGVNPGDRAYFQAVRQLCDQRRMLLILDEVQVGMGRSGQLWGYENL 260 Query: 259 GIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEE 318 GI PD T AK +GGG PI + KA + + G T+ G+P+AC A LA+ +V E Sbjct: 261 GIEPDAFTVAKGLGGGVPIGALLVKAS-CNILQAGEHASTFGGNPLACRAGLAIAQVMER 319 Query: 319 EKLLERSQAVGERLKAGLREIQAKH-KVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKI 377 ++LL QA GE+L+AGL+E+ ++ ++ VRG G + + L + A + Sbjct: 320 DQLLANVQARGEQLRAGLQELVDRYPNLLAGVRGWGLINGLVLRNDPNVTPIA------L 373 Query: 378 VVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAI 417 V A E+GL+L+ G V+RF+ P+ + A++++ LA+ Sbjct: 374 VKAAIEQGLLLVPAGA--EVVRFVPPLIVSAAEIDEALAM 411 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: 444 Number of extensions: 21 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: 422 Length adjustment: 32 Effective length of query: 394 Effective length of database: 390 Effective search space: 153660 Effective search space used: 153660 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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