Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate AZOBR_RS19025 AZOBR_RS19025 acetylornithine aminotransferase
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__azobra:AZOBR_RS19025 Length = 389 Score = 193 bits (491), Expect = 7e-54 Identities = 137/416 (32%), Positives = 197/416 (47%), Gaps = 57/416 (13%) Query: 26 VVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTC--FQVLA 83 +V ER E ++ +GR ++DFA G+AV GH +P ++ A+ Q KL HT F+V Sbjct: 14 IVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTSNLFRVAG 73 Query: 84 YEPYIELAEEIAKRVP-GDFPKKTLLVTSGSEAVENAVKIAR------AATGRAGVIAFT 136 E +AKR+ F SG+EA E K+ R R +I F Sbjct: 74 QE-------SLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIITFE 126 Query: 137 GAYHGRTMMTLGLTG--KVV----PYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIER 190 A+HGRT+ + K++ P G L+P G A+ Sbjct: 127 QAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAV------------------- 167 Query: 191 IFKNDAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTG 250 +A + A I +EP+QGEGG S F++ LR +CD+HG+LL DE+Q G GRTG Sbjct: 168 ---RNAVTDETAGICLEPIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTG 224 Query: 251 TFFATEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAAL 310 FA E GI PD+ AK +GGGFP+ + + G G TY G+P+A A Sbjct: 225 KLFAHEWAGITPDVMAVAKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGN 284 Query: 311 AVLKVFEEEKLLERSQAVGERLKAGLREIQAKH-KVIGDVRGLGSMVAIELFEGGDTHKP 369 AVL E L+ Q +G L+ L + A++ V VRG G M+ + Sbjct: 285 AVLDKVLEPGFLDHVQRIGGLLQDRLAGLVAENPAVFKGVRGKGLMLGL----------A 334 Query: 370 AAELVSKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAECFDEL 425 V +VV R GL+ + G NV+R L P+ I +A++E+ +AILA+ EL Sbjct: 335 CGPAVGDVVVALRANGLLSVPAGD--NVVRLLPPLNIGEAEVEEAVAILAKTAKEL 388 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: 451 Number of extensions: 22 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: 389 Length adjustment: 31 Effective length of query: 395 Effective length of database: 358 Effective search space: 141410 Effective search space used: 141410 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