Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_013450014.1 SULKU_RS13855 aspartate aminotransferase family protein
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_000183725.1:WP_013450014.1 Length = 388 Score = 166 bits (421), Expect = 9e-46 Identities = 120/373 (32%), Positives = 192/373 (51%), Gaps = 25/373 (6%) Query: 68 WQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQEL--LDPL 125 ++ G TL D++G+E+ID G + +VGH N + A+ +Q AK LH L ++P Sbjct: 17 FERGDNATLCDSEGKEYIDFAAGVAVCSVGHGNCRLARAISDQAAKI-LHVSNLYRIEP- 74 Query: 126 RAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAFHG 182 + A+ + L+ ++ FF NSGTE+ E A+K+A+ Y G ++ I +FHG Sbjct: 75 QEECARRIVELSGYDMR-CFFGNSGTEANEGAIKIARKYGERDGSIKRYKIITLENSFHG 133 Query: 183 KSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQG 242 +++ AL AT +++ F P GF + N+E + + ++E AV++E +QG Sbjct: 134 RTITALKATGQASKHDYFGPYPDGFVYA--ANVEEIESLIDET------TVAVMIELVQG 185 Query: 243 EGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKAL 302 EGGV + + L L+I+DEVQTG+ R G A + + PD++ LAK L Sbjct: 186 EGGVQPLDKQKVQNLSALLKSKDILLIVDEVQTGIYRCGSFLASHYYGITPDVITLAKGL 245 Query: 303 GGGVMPIGATIA-TEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQ 361 GGGV PIG + +E+FS H +TFGGN L+ AA +++L N + + Sbjct: 246 GGGV-PIGVVMTRLKEIFSY-----GDHGSTFGGNYLSTVAANEVLDILEAYNKSGEMME 299 Query: 362 KGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNN 421 + + A YPD+ E G GM+ + +D+E+ F VLV + N Sbjct: 300 HQNYFETSLKSFALHYPDIFTERVGIGMMQGLRVIDSEVLSKIIDSAFEIGVLVIKSGRN 359 Query: 422 AKTIRIEPPLTLT 434 T+R PPLT++ Sbjct: 360 --TLRFVPPLTIS 370 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: 380 Number of extensions: 24 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: 388 Length adjustment: 32 Effective length of query: 427 Effective length of database: 356 Effective search space: 152012 Effective search space used: 152012 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: 50 (23.9 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