Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate Echvi_0577 Echvi_0577 ornithine aminotransferase
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Cola:Echvi_0577 Length = 413 Score = 209 bits (531), Expect = 2e-58 Identities = 127/384 (33%), Positives = 203/384 (52%), Gaps = 35/384 (9%) Query: 78 DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQ----ELLDPLRAMLAKTL 133 D +G+++ D L + N GH +P ++ + +Q L S+ ++L P L + Sbjct: 40 DVEGEKYYDFLSSYSAVNQGHCHPRILQTLIDQAGTLTLTSRAFHNDVLGPFEKFLTEYF 99 Query: 134 A--ALTPGKLKYSFFCNSGTESVEAALKLAK--AYQS---PRGKFTFIATSGAFHGKSLG 186 + P N+G E VE A+K+A+ Y+ P + T I FHG++ Sbjct: 100 GYDKVLP--------MNTGAEGVETAIKIARKWGYEKKGIPENEGTIIVAKNNFHGRTTT 151 Query: 187 ALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGV 246 +S + T RK F P PGF +P +I+A++ L++ K ++ ++EPIQGE GV Sbjct: 152 VISFSNDETARKNFGPYTPGFVTIPHDDIDALKDVLSQSK----NIIGYLVEPIQGEAGV 207 Query: 247 ILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGV 306 +P GYL V +C + G L + DE+QTG+ RTGK+ AC+HE V+PD+L L KA+ GG Sbjct: 208 YVPKEGYLKEVAAVCKDHGVLFMADEIQTGIARTGKLLACDHEGVKPDMLILGKAISGGF 267 Query: 307 MPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDML 366 P+ A +A + + V+ P H +TFGGNPL A+ +NV+ ++ L A++ G + Sbjct: 268 YPVSAVLADDHIMEVI--QPGQHGSTFGGNPLGAKVAMTALNVVKDEKLAENADKLGKLF 325 Query: 367 LDGFRQLAREYPDLVQEARGKGMLMAI---EFVDNEIGYNFASEMFRQRVLVAGTLNNAK 423 + +QL + DLV+ RGKG+L AI + D++ + + +L T N Sbjct: 326 RERIQQLV-DKSDLVELVRGKGLLNAIVINDTEDSDTAWRLCLALKENGLLAKPTHGN-- 382 Query: 424 TIRIEPPLTLTIEQ----CELVIK 443 IR PPL +T EQ C+++ K Sbjct: 383 IIRFAPPLVITEEQLHDCCDIIEK 406 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: 429 Number of extensions: 35 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: 413 Length adjustment: 32 Effective length of query: 427 Effective length of database: 381 Effective search space: 162687 Effective search space used: 162687 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