Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate SMc02413 SMc02413 aminotransferase
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__Smeli:SMc02413 Length = 437 Score = 241 bits (614), Expect = 4e-68 Identities = 140/390 (35%), Positives = 213/390 (54%), Gaps = 7/390 (1%) Query: 40 EGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYIELAEEIAKRVP 99 +GR+ +DF+ + GH HP + AV L + + A E + LAE++ VP Sbjct: 37 DGRQLLDFSASWGAASLGHSHPAIREAVGRALSDQAGASYLSSANEACVLLAEKLLSLVP 96 Query: 100 GDFPKKTLLVTSGSEAVENAVKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSA- 158 + SGS+A E +I AATGR ++AF GAYHG T+ ++G++G + Sbjct: 97 ERARGRVWFGHSGSDANETVARIVVAATGRPRILAFHGAYHGGTIGSMGVSGHPAQQGSR 156 Query: 159 --GMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQDIAAIIIEPVQGEGGFY 216 G+ L+P A E + D ++A +ER+F + P+++AA IEP+Q +GG Sbjct: 157 AEGLTLVPYPNSYAAGSPE---AARDAALAHLERLFATEVPPEEVAAFFIEPIQSDGGML 213 Query: 217 VNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLGIVPDLTTFAKSVGGGFP 276 V F + + ALC +HGIL+++DEV+ G GR+G F A E GI PD+ F K +GGG P Sbjct: 214 VPPDGFFKAVEALCRRHGILIVSDEVKVGLGRSGRFNAFEHSGIEPDIVVFGKGLGGGLP 273 Query: 277 ISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEEKLLERSQAVGERLKAGL 336 IS V G IM+ L T G+P+ AAALAVL+ E + L+ + G+ L+ L Sbjct: 274 ISAVVGPEAIMNHSVAFSL-QTVHGNPVCAAAALAVLQTIERDHLILNADRSGKVLREAL 332 Query: 337 REIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVVRAREKGLILLSCGTYYN 396 + A+H +IGDVRG G + IEL + +PA+ + V RA + GL+L G N Sbjct: 333 DRLTARHTLIGDVRGRGLALGIELVTDPASREPASRQAALTVYRAFQLGLVLYYVGVQSN 392 Query: 397 VIRFLMPVTIPDAQLEKGLAILAECFDELA 426 V+ P+T+ A+ E G+A+L + ++A Sbjct: 393 VLELTPPLTLTPAEAESGVAMLGQALADVA 422 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: 482 Number of extensions: 24 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: 437 Length adjustment: 32 Effective length of query: 394 Effective length of database: 405 Effective search space: 159570 Effective search space used: 159570 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 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