Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_011911296.1 PST_RS00235 aspartate aminotransferase family protein
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_000013785.1:WP_011911296.1 Length = 439 Score = 187 bits (476), Expect = 5e-52 Identities = 128/393 (32%), Positives = 196/393 (49%), Gaps = 39/393 (9%) Query: 79 TQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQ-ELLDPLRAMLAKTLAALT 137 + G++ +D G N GH + AV Q+A+ ++ PL LA+ LAA++ Sbjct: 40 SDGRQVLDGTAGLWCCNAGHGRREISEAVSKQIARMDFAPTFQMGHPLPFELAEKLAAIS 99 Query: 138 PGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFT---FIATSGAFHGKSLGALSATAKS 194 P L FF NSG+ES + ALK+A AYQ G+ + I A+HG G +S + Sbjct: 100 PEGLNRVFFTNSGSESADTALKIALAYQRAIGQGSRTRLIGRELAYHGVGFGGMSVGGMA 159 Query: 195 TFRKPFMPLLPGFRHVPFGNIEAMRTALNE-----------------CKKTGDDVAAVIL 237 R+ F P+LPG H+P ++ R A ++ +++AAVI+ Sbjct: 160 NNRRAFGPMLPGVDHLPH-TLDLQRNAFSKGLPQHGVERADELERLVTLHGAENIAAVIV 218 Query: 238 EPIQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILC 297 EP+ G GVILPP GYL +R++ + G L+I DEV TG GR G+ FA + V PDIL Sbjct: 219 EPMSGSAGVILPPVGYLQRLREITAKHGILLIFDEVITGFGRVGEAFAAQRWGVTPDILT 278 Query: 298 LAKALGGGVMPIGATIATEEVFSVLFDNP-----FLHTTTFGGNPLACAAALATINVLLE 352 AK L G +P+GA + ++ P F H T+ G+P+ACAAALAT + + Sbjct: 279 CAKGLTNGAIPMGAVFVADRLYDAFMQGPESVIEFFHGYTYSGHPVACAAALATQQIYQQ 338 Query: 353 QNLPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDN-----EIGYNFASE 407 +NL +A + L R+ P+++ + R G++ I+F + + GY E Sbjct: 339 ENLFQKAIDLEPYWQEALFSL-RDLPNVI-DIRTVGLVAGIQFAAHADGVGKRGYEVFRE 396 Query: 408 MFRQRVLVAGTLNNAKTIRIEPPLTLTIEQCEL 440 F +LV + TI + P L +E+ E+ Sbjct: 397 CFENGLLVRA---SGDTIALSP--ALIVEKAEI 424 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: 419 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: 439 Length adjustment: 33 Effective length of query: 426 Effective length of database: 406 Effective search space: 172956 Effective search space used: 172956 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 Apr 09 2024. 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