Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate GFF2829 PGA1_c28750 aminotransferase class-III
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >FitnessBrowser__Phaeo:GFF2829 Length = 440 Score = 191 bits (485), Expect = 3e-53 Identities = 127/361 (35%), Positives = 189/361 (52%), Gaps = 33/361 (9%) Query: 5 VMPTYARADI-VFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLW 63 V P + +AD+ G+G YL +G+R+LD + G AV+ LGH++ ++ A+ Q KL Sbjct: 4 VFPRHTKADLPTAVAGDGCYLIDANGKRYLDGSGGAAVSCLGHSDAEVIAAVQEQVGKLA 63 Query: 64 HTSNLFRVAGQ-ESLAKRLTEATFADT--VFFTNSGAEAWECGAKLIRKYHYEKGDKART 120 F + E+LA L D V+F + G+EA E KL R+YH E+GD R Sbjct: 64 FAHTGFLTSEPAEALADLLISQAPGDLHRVYFVSGGSEATEAAIKLARQYHLERGDTTRR 123 Query: 121 RIITFEQAFHGRTLAAVSAAQQEKLIKGFGPLL----------------DGFDLVPFG-- 162 +I Q++HG TL A++A + F PLL DG +G Sbjct: 124 HVIARRQSYHGNTLGALAAGGNAWRRQQFAPLLIDISHIAPCYEYVDRGDGESRYDYGQR 183 Query: 163 ---DLEAVRNAVTDETA-GICLEPIQGEGGIRAGSVE-FLRGLREICDEHGLLLFLDEIQ 217 +LEA + ET EP+ G +VE + + +REICD++G+LL LDE+ Sbjct: 184 VANELEAEILRLGPETVMAFMAEPVVGATSGAVPAVEGYFKRIREICDQYGVLLILDEVM 243 Query: 218 CGMGRTGKLFAHEWAGITPDVMAVAKGIGGGF-PLGACLATEKAASGMTAGT----HGST 272 CGMGRTG LFA E G+ PD++ +AKG+G G+ P+GA L + + + G+ HG T Sbjct: 244 CGMGRTGHLFACEADGVAPDILCIAKGLGAGYQPIGAMLCSRQIYDAIEGGSGFFQHGHT 303 Query: 273 YGGNPLATAVGNAVLDKVLEPGFLDHVQRIGGLLQDRLAGLVAENPAVFKGVRGKGLMLG 332 Y G+P+ATA G AV+ +L+ G + +G L L ++P V +RG+GL G Sbjct: 304 YIGHPVATAAGLAVVRALLDRGLVQRSAEMGETLHAALVARFGQHPHV-GDLRGRGLFRG 362 Query: 333 L 333 + Sbjct: 363 I 363 Lambda K H 0.321 0.139 0.414 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: 480 Number of extensions: 32 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: 389 Length of database: 440 Length adjustment: 31 Effective length of query: 358 Effective length of database: 409 Effective search space: 146422 Effective search space used: 146422 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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