Align Putrescine aminotransferase; PAT; PATase; EC 2.6.1.82; Cadaverine transaminase; EC 2.6.1.-; Putrescine transaminase; Putrescine--2-oxoglutaric acid transaminase (uncharacterized)
to candidate WP_022949042.1 H035_RS0111080 acetylornithine transaminase
Query= curated2:B7LZM2 (459 letters) >NCBI__GCF_000421465.1:WP_022949042.1 Length = 389 Score = 238 bits (608), Expect = 2e-67 Identities = 147/371 (39%), Positives = 221/371 (59%), Gaps = 21/371 (5%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQEL--LDPLRAMLAKTV 133 L DTQG+ ++D + G + N+GH +P + A+ +Q +++ H+ L ++P A LA+T+ Sbjct: 24 LWDTQGKRYLDAISGIAVCNLGHAHPTLARALCDQ-SQRLWHTSNLYRIEPQEA-LAETL 81 Query: 134 AALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFT--FIATSGAFHGKSLGALSAT 191 L+ ++ FFCNSG E+ EAALK+A+AY +G T + +FHG++L LSAT Sbjct: 82 TRLSG--MENVFFCNSGAEANEAALKIARAYGHLQGIDTPRVVVADQSFHGRTLATLSAT 139 Query: 192 AKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPP 251 ++ F PLLPGF VPFG+ A+ + DV AV++EPIQGEGGV +PP Sbjct: 140 GNPRIQQGFEPLLPGFLRVPFGDPNAVAVLEDR-----SDVVAVLVEPIQGEGGVRMPPN 194 Query: 252 GYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGA 311 GYL +R+LCD G L++LDEVQTG+GRTG+ F +HE V PD++ LAK+LG G PIGA Sbjct: 195 GYLAELRRLCDRNGWLLMLDEVQTGIGRTGRWFGGQHEAVTPDVMTLAKSLGNG-FPIGA 253 Query: 312 TIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFR 371 +A + VL H +TFGGN L C AL + ++ ++ L +A + GD L + Sbjct: 254 CLAKGKAAEVL--TAGRHGSTFGGNFLGCRVALEVLRIIEQEGLIDRAARLGDQLKEALA 311 Query: 372 QLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPL 431 +P V+ RG+G+++AIE +D+ + E + +L+ T N +R+ PPL Sbjct: 312 HRLGRHPQ-VKNIRGRGLILAIE-LDHPCAH-LVPEALERGLLINVTATN--VLRLLPPL 366 Query: 432 TLTIEQCELVI 442 L Q E ++ Sbjct: 367 ILENSQAEQLV 377 Lambda K H 0.320 0.136 0.395 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: 413 Number of extensions: 21 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: 389 Length adjustment: 32 Effective length of query: 427 Effective length of database: 357 Effective search space: 152439 Effective search space used: 152439 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