Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate GFF3766 HP15_3708 4-aminobutyrate aminotransferase
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__Marino:GFF3766 Length = 425 Score = 348 bits (894), Expect = e-100 Identities = 180/398 (45%), Positives = 247/398 (62%), Gaps = 4/398 (1%) Query: 20 HGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLA 79 H NAE+WD DGKR IDF GGIGVLN+GH +P VVEA++AQ +L H P+ Y+ Sbjct: 28 HATNAELWDADGKRMIDFAGGIGVLNIGHRHPKVVEAVKAQLDKLMHTCQTVMPYEGYVK 87 Query: 80 LMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHGRTLATLNL 139 L E+LS VPV ML NSGAEA ENA+K+AR ATGK +I FDGG+HGRT T+ + Sbjct: 88 LAEKLSGVVPVRGHAKVMLANSGAEALENAMKIARAATGKTNVICFDGGYHGRTFYTMAM 147 Query: 140 NGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVEDVAAFIFEPV 199 NGK APY+ G +PG VY PYP GV+ ++AL+ + + + AA + EPV Sbjct: 148 NGKAAPYQTDFGPMPGTVYRAPYPVPYHGVSEDEALRGLKMAMKADSPAHNTAAIVIEPV 207 Query: 200 QGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPDLLLLAK 259 GEGGF A +F + +R+ CDE IL+I DE+QSGFGRTG+ FA G+EPDL+ +AK Sbjct: 208 LGEGGFYAAPTSFLKEIRKICDENDILMIADEVQSGFGRTGKMFAIEHSGVEPDLMTMAK 267 Query: 260 SIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLATWGERQE 319 S+A GMP+ A+VG + M A LGGTY+G+P +CAAALA +E++ + Sbjct: 268 SMADGMPISAIVGTDKYMDASGPNSLGGTYTGSPTACAAALAVFDVFKEEDILGKSQALG 327 Query: 320 QAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGS--PAPAQLAKVMEAARARGLL 377 + + R+ +W+ ++ + +G M E + S P P A V + A+ +GL+ Sbjct: 328 EKLKQRFSQWQEQ--FAHVDNVRNLGPMAAFELVESKESRTPKPELAAAVTKKAKEKGLI 385 Query: 378 LMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 L+ G + +R L P+TIE EVLEEGL I+E+ L E+ Sbjct: 386 LLSCGMYGNTLRFLMPVTIEDEVLEEGLAIVEESLKEV 423 Lambda K H 0.320 0.137 0.402 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: 518 Number of extensions: 29 Number of successful extensions: 3 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: 416 Length of database: 425 Length adjustment: 32 Effective length of query: 384 Effective length of database: 393 Effective search space: 150912 Effective search space used: 150912 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