Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_011778553.1 MVAN_RS06505 ornithine--oxo-acid transaminase
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_000015305.1:WP_011778553.1 Length = 403 Score = 214 bits (546), Expect = 3e-60 Identities = 132/374 (35%), Positives = 198/374 (52%), Gaps = 25/374 (6%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAA 135 + D +G+ ++DCL + N GHRNP V++ QL L S+ A LA Sbjct: 39 ITDVEGRRYLDCLAAYSAVNFGHRNPEVIATAHAQLDAVTLVSRAFHSDRLAPFCAALAD 98 Query: 136 LTPGKLKYSFFCNSGTESVEAALKLAKAYQ-SPRGKFT--FIATSGAFHGKSLGALSATA 192 L + NSG E+VE+ +K+A+ + +G T + FHG++ +S + Sbjct: 99 LCGKDMVLPM--NSGAEAVESGIKVARKWGVDVKGVKTPNIVVAHNNFHGRTTTIISFSD 156 Query: 193 KSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPG 252 T R+ F P PGFR VPFG+ +A+ A++ DD AV++EPIQGE G+I+PP Sbjct: 157 DETARRGFGPYTPGFRSVPFGDADALAPAVD------DDTVAVLIEPIQGEAGIIVPPDD 210 Query: 253 YLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGAT 312 YL VR LC E LMI DE+Q+G+ RTG+ FAC+H V PDI L KALGGGV+P+ A Sbjct: 211 YLPRVRALCTERNVLMIADEIQSGLARTGRTFACDHWGVVPDIYLLGKALGGGVLPLSAV 270 Query: 313 IATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDML---LDG 369 +A ++ VL +P H +TFGGNPLA A +++L ++ + G L L+G Sbjct: 271 VADRDILGVL--HPGEHGSTFGGNPLAAAIGSTVVDILRRGEFQRRSTELGAHLHARLNG 328 Query: 370 FRQLAREYPDLVQEARGKGMLMAIEF-VDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIE 428 + V RG+G+ ++ + G + + + VLV T + T+R Sbjct: 329 LKGRG------VLAVRGRGLWAGVDIDPAHGTGKQVSLRLAERGVLVKDT--HGSTLRFA 380 Query: 429 PPLTLTIEQCELVI 442 PPL +T ++ + I Sbjct: 381 PPLVITADEIDWAI 394 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: 410 Number of extensions: 15 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: 403 Length adjustment: 32 Effective length of query: 427 Effective length of database: 371 Effective search space: 158417 Effective search space used: 158417 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 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