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) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4910 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:
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