Align Putrescine aminotransferase; PAT; PATase; EC 2.6.1.82; Cadaverine transaminase; EC 2.6.1.-; Putrescine transaminase; Putrescine--2-oxoglutaric acid transaminase (uncharacterized)
to candidate WP_076476008.1 BW971_RS02060 4-aminobutyrate--2-oxoglutarate transaminase
Query= curated2:B7LZM2 (459 letters) >NCBI__GCF_900156495.1:WP_076476008.1 Length = 452 Score = 177 bits (449), Expect = 6e-49 Identities = 135/393 (34%), Positives = 202/393 (51%), Gaps = 41/393 (10%) Query: 71 GGLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLA 130 GG+ +VD G ID G + VG NP V AV Q A H+ ++ P +A Sbjct: 52 GGI--IVDVDGNSLIDLGSGIAVTGVGASNPAVADAVAAQ-AHHFTHTCFMVTPYEGYVA 108 Query: 131 --KTVAALTPGKL-KYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGA 187 + + LTPG K S NSG E+VE A+K+A+ G+ +A A+HG++ Sbjct: 109 VAEKLNELTPGDHEKRSVLFNSGAEAVENAVKVARL---ATGRDAIVAFDHAYHGRTNLT 165 Query: 188 LSATAKST-FRKPFMPLLPGFRHVPFG----------NIEAMRTALNECKKT--GDDVAA 234 ++ TAK+ ++ F P P +P + A + A+ + + G+ VA Sbjct: 166 MALTAKTQPYKYNFGPFAPEIYRMPMSYPYRDDLGTDGVSAAKRAIRQIETQIGGEAVAG 225 Query: 235 VILEPIQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPD 294 +++EPIQGEGG I+P PG+LT + + + G + I DEVQ G RTG FA E E + PD Sbjct: 226 LLIEPIQGEGGFIVPAPGFLTTLAEWARDNGVVFIADEVQAGFCRTGTWFASEAEGIVPD 285 Query: 295 ILCLAKALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQN 354 I+ AK + GG MP+ A ++ + +P T+GGNP+ACAAALATI + E + Sbjct: 286 IVTTAKGIAGG-MPLSAITGRADLLDKV--HPGGLGGTYGGNPVACAAALATIAEMEELD 342 Query: 355 LPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRV- 413 L A+A ++ L R LA + D++ + RG+G ++AIE V E G + + ++V Sbjct: 343 LNARAHHIEEIALPRLRTLADDL-DVIGDVRGRGAMLAIEIV--EPGTDTPAPALAKKVA 399 Query: 414 ----------LVAGTLNNAKTIRIEPPLTLTIE 436 LV GT N IR+ PPL + E Sbjct: 400 AAALEAGVVILVTGTFGN--VIRLLPPLVIDDE 430 Lambda K H 0.320 0.136 0.395 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: 528 Number of extensions: 29 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: 459 Length of database: 452 Length adjustment: 33 Effective length of query: 426 Effective length of database: 419 Effective search space: 178494 Effective search space used: 178494 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 24 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