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_015944558.1 DHAF_RS16705 glutamate-1-semialdehyde 2,1-aminomutase
Query= curated2:B7LZM2 (459 letters) >NCBI__GCF_000021925.1:WP_015944558.1 Length = 430 Score = 137 bits (345), Expect = 7e-37 Identities = 99/309 (32%), Positives = 153/309 (49%), Gaps = 19/309 (6%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTVAA 135 L D G ++D + +G +GH +PVVV A++ A + S + A+ V Sbjct: 48 LWDIDGNSYLDYVLSWGPLILGHAHPVVVGAIK--AAAERGTSYGAPTEIETECAEEVIK 105 Query: 136 LTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGK--SLGALSATAK 193 P ++ +SGTE+ +AL+LA+ G+ I G +HG SL + + Sbjct: 106 AFPS-MEMVRMVSSGTEATMSALRLARGVT---GRNKIIKFEGCYHGHGDSLLIKAGSGA 161 Query: 194 STFRKPFMPLLPGFRH-----VPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVIL 248 TF P P +P + ++E ++ EC G+D+AAVILEP+ G GV+L Sbjct: 162 LTFGVPTSPGVPSSVASQTIVAQYNDLEGLKEIFKEC---GEDIAAVILEPVTGNMGVVL 218 Query: 249 PPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMP 308 P PG+L +R L ++G+L+I DEV TG R A + PD+ CL K +GGG +P Sbjct: 219 PQPGFLAGLRTLTQDYGSLLIFDEVMTGF-RVSYGGAQGRYQIDPDLTCLGKVIGGG-LP 276 Query: 309 IGATIATEEVF-SVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLL 367 + A + V P T GNPLA AA LAT+ +L ++ + E+K L Sbjct: 277 VAAYGGKRKYMEQVAPSGPIYQAGTLSGNPLAMAAGLATLKLLQQEGVYEGLEKKTARLA 336 Query: 368 DGFRQLARE 376 +G + +A+E Sbjct: 337 EGLQSIAQE 345 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: 430 Number of extensions: 13 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: 430 Length adjustment: 32 Effective length of query: 427 Effective length of database: 398 Effective search space: 169946 Effective search space used: 169946 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