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 15866 b1748 succinylornithine transaminase, PLP-dependent (NCBI)
Query= curated2:B7LZM2 (459 letters) >FitnessBrowser__Keio:15866 Length = 406 Score = 193 bits (491), Expect = 8e-54 Identities = 127/369 (34%), Positives = 191/369 (51%), Gaps = 23/369 (6%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAK-QPLHSQELLDPLRAMLAKTVA 134 L D QG+E+ID GG + +GH +P + A+ Q +K + +P+ + K + Sbjct: 33 LWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTNEPVLRLAKKLID 92 Query: 135 ALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPR---GKFTFIATSGAFHGKSLGALSAT 191 A ++ FFCNSG E+ EAALKLA+ + R K +A AFHG++L +SA Sbjct: 93 ATFADRV---FFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNAFHGRTLFTVSAG 149 Query: 192 AKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPP 251 + + + F PL RH + +I + ++ D AVI+EPIQGEGGV+ Sbjct: 150 GQPAYSQDFAPLPADIRHAAYNDINSASALID------DSTCAVIVEPIQGEGGVVPASN 203 Query: 252 GYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGA 311 +L +R+LC+ AL+I DEVQTG+GRTG+++A H V PD+L AKALGGG P+GA Sbjct: 204 AFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLTTAKALGGG-FPVGA 262 Query: 312 TIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFR 371 +ATEE V+ H TT+GGNPLA A A + ++ + +Q+ D ++ Sbjct: 263 LLATEECARVM--TVGTHGTTYGGNPLASAVAGKVLELINTPEMLNGVKQRHDWFVERLN 320 Query: 372 QLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGT---LNNAKTIRIE 428 + Y L E RG G+L+ Y ++ Q AG + +R Sbjct: 321 TINHRY-GLFSEVRGLGLLIGCVL---NADYAGQAKQISQEAAKAGVMVLIAGGNVVRFA 376 Query: 429 PPLTLTIEQ 437 P L ++ E+ Sbjct: 377 PALNVSEEE 385 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: 441 Number of extensions: 28 Number of successful extensions: 6 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: 406 Length adjustment: 32 Effective length of query: 427 Effective length of database: 374 Effective search space: 159698 Effective search space used: 159698 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 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