Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_076476008.1 BW971_RS02060 4-aminobutyrate--2-oxoglutarate transaminase
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_900156495.1:WP_076476008.1 Length = 452 Score = 178 bits (451), Expect = 4e-49 Identities = 134/388 (34%), Positives = 199/388 (51%), Gaps = 39/388 (10%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLA--KTL 133 +VD G ID G + VG NP V AV Q A H+ ++ P +A + L Sbjct: 55 IVDVDGNSLIDLGSGIAVTGVGASNPAVADAVAAQ-AHHFTHTCFMVTPYEGYVAVAEKL 113 Query: 134 AALTPGKL-KYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATA 192 LTPG K S NSG E+VE A+K+A+ G+ +A A+HG++ ++ TA Sbjct: 114 NELTPGDHEKRSVLFNSGAEAVENAVKVARL---ATGRDAIVAFDHAYHGRTNLTMALTA 170 Query: 193 KST-FRKPFMPLLPGFRHVPFG----------NIEAMRTALNECKKT--GDDVAAVILEP 239 K+ ++ F P P +P + A + A+ + + G+ VA +++EP Sbjct: 171 KTQPYKYNFGPFAPEIYRMPMSYPYRDDLGTDGVSAAKRAIRQIETQIGGEAVAGLLIEP 230 Query: 240 IQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLA 299 IQGEGG I+P PG+LT + + + G + I DEVQ G RTG FA E E + PDI+ A Sbjct: 231 IQGEGGFIVPAPGFLTTLAEWARDNGVVFIADEVQAGFCRTGTWFASEAEGIVPDIVTTA 290 Query: 300 KALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQA 359 K + GG MP+ A ++ + +P T+GGNP+ACAAALATI + E +L A+A Sbjct: 291 KGIAGG-MPLSAITGRADLLDKV--HPGGLGGTYGGNPVACAAALATIAEMEELDLNARA 347 Query: 360 EQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRV------ 413 ++ L R LA + D++ + RG+G ++AIE V E G + + ++V Sbjct: 348 HHIEEIALPRLRTLADDL-DVIGDVRGRGAMLAIEIV--EPGTDTPAPALAKKVAAAALE 404 Query: 414 -----LVAGTLNNAKTIRIEPPLTLTIE 436 LV GT N IR+ PPL + E Sbjct: 405 AGVVILVTGTFGN--VIRLLPPLVIDDE 430 Lambda K H 0.320 0.135 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: 516 Number of extensions: 28 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