Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate PfGW456L13_4910 Acetylornithine aminotransferase (EC 2.6.1.11)
Query= BRENDA::P42588 (459 letters) >lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4910 Acetylornithine aminotransferase (EC 2.6.1.11) Length = 413 Score = 222 bits (565), Expect = 2e-62 Identities = 144/397 (36%), Positives = 216/397 (54%), Gaps = 30/397 (7%) Query: 65 AVEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLD- 123 A+ + G L D G+E++D + G + NVGH +P +V+A+ Q A LH+ L Sbjct: 36 ALSFNKGLGTRLWDQAGREYLDAVAGVAVTNVGHSHPKIVAAITEQ-AGLLLHTSNLYSI 94 Query: 124 PLRAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG--KFTFIATSGAFH 181 + LA+ L L + +FF NSG E+ E ALK+A+ + +G + + AFH Sbjct: 95 DWQQRLAQKLTQLAG--MDRAFFNNSGAEANETALKIARLHGWHKGIEQPLVVVMENAFH 152 Query: 182 GKSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQ 241 G++LG LSA+ R F L F VPFG++ A+ + G + AV++EPIQ Sbjct: 153 GRTLGTLSASDGPAVRLGFNKLPGDFVKVPFGDLGALDKVQ---QAFGSRIVAVLMEPIQ 209 Query: 242 GEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKA 301 GE GV L PPGYL+AVR+LC+ L++LDE+QTG+GRTG+ FA +HE + PD++ LAK Sbjct: 210 GESGVQLAPPGYLSAVRELCNRRSWLLMLDEIQTGIGRTGQWFAFQHEGIVPDVMTLAKG 269 Query: 302 LGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQ 361 LG GV PIGA +A + + P H +TFGGNPLAC ++++ EQ L A Sbjct: 270 LGNGV-PIGACLARGKAAELF--TPGSHGSTFGGNPLACRVGCTVLDIVEEQGLLENARL 326 Query: 362 KGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAG---- 417 +G LL+ R P+ V + RG+G+++ IE + R L+A Sbjct: 327 QGARLLERLRTELAGNPN-VSQIRGQGLMIGIEL----------KQPIRDLSLIAARDHG 375 Query: 418 ---TLNNAKTIRIEPPLTLTIEQCELVIKAARKALAA 451 + TIR+ PPLTL + E++++ + + A Sbjct: 376 LLINVTRGNTIRLLPPLTLDEREVEMIVRGVGRVVNA 412 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: 434 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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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