Align 2-oxoadipate decarboxylase/hydroxylase (2-hydroxyglutarate synthase) (characterized)
to candidate WP_090438598.1 BLS63_RS01105 DUF1338 domain-containing protein
Query= reanno::Putida:PP_5260 (464 letters) >NCBI__GCF_900100495.1:WP_090438598.1 Length = 475 Score = 578 bits (1491), Expect = e-169 Identities = 305/457 (66%), Positives = 352/457 (77%), Gaps = 4/457 (0%) Query: 6 FVSPDSIRAQFSAAMSLMYKQEVPLYGTLLELVSEINQQVMAQQPEVAEALRWTGEIERL 65 +V PD IRAQFS AMS MY+ EVPLYG LLELV E+N+Q +AQ E+AE LR TGEI+RL Sbjct: 12 WVHPDEIRAQFSRAMSAMYQAEVPLYGELLELVGEVNRQALAQDGELAERLRLTGEIQRL 71 Query: 66 DQERHGAIRVGTAEELATIARLFAVMGMQPVGYYDLSSAGVPVHSTAFRAVHEQSLHVSP 125 D ERHGAIR+G+A ELAT+ RLFAV+GM PVGYYDLS AGVPVH+TAFRA+HE SL P Sbjct: 72 DMERHGAIRLGSATELATMRRLFAVLGMSPVGYYDLSCAGVPVHATAFRAIHEGSLQHCP 131 Query: 126 FRVFTSLLRLELIDNPQLRELAQSILAKRQIFTSRALELIAQCEREGGLDAADAETFVQE 185 FRVFTSLLRLELI++ LRELA IL +R IFT+RALELI + E+ GGLD +A F+++ Sbjct: 132 FRVFTSLLRLELIEDAPLRELASDILGRRSIFTARALELIERFEQAGGLDRGEAGEFIEQ 191 Query: 186 ALHTFRWHQDATVTAEQYQQLHDQHRLIADVVAFKGPHINHLTPRTLDIDAIQLGMPAKG 245 AL TFRWH++ATV A Y+QL QHRLIADVVAFKGPHINHLTPR+LDIDA+Q GMP +G Sbjct: 192 ALETFRWHREATVGAALYRQLSAQHRLIADVVAFKGPHINHLTPRSLDIDAVQAGMPRRG 251 Query: 246 IPPKAVVEGPPTRRHPILLRQTSFKALQETVAFRDQQGRE--GSHTARFGEIEQRGAALT 303 I PKA+VEGPP RR PILLRQTSFKAL E V F + G GSH+ARFGEIEQRGAALT Sbjct: 252 IDPKAIVEGPPARRCPILLRQTSFKALHEQVLFVEDNGERALGSHSARFGEIEQRGAALT 311 Query: 304 PKGRQLYDKLLDATRVALGGA-PAEANAERYMALLQANFAEFPDDLAQMREQGLAYFRYF 362 KGR LYD+LLD R A GA P +ANA Y L A F EFPDD A +R QGLAYFRYF Sbjct: 312 AKGRALYDRLLDGARQASAGASPEQANA-AYRQALVAQFGEFPDDYASLRRQGLAYFRYF 370 Query: 363 ATEKGLAARDQEGRPTTLQGLIDAGHVHFEALVYEDFLPVSAAGIFQSNLGDDAQAEYGS 422 + GL A+ + L+ L+ AGHV E LVYEDFLPVSAAGIFQSNLGD A+ Y Sbjct: 371 VSPAGLTAKARGELAGDLETLLAAGHVCCEPLVYEDFLPVSAAGIFQSNLGDAARDSYAH 430 Query: 423 NANREAFEAALGLQVQDELALYAQSERRSLQACAQAL 459 +AN++AFE LG V DELALYA ++RRSL CA+ L Sbjct: 431 SANQDAFERDLGAPVYDELALYADTQRRSLAQCAEQL 467 Lambda K H 0.319 0.133 0.378 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: 690 Number of extensions: 20 Number of successful extensions: 3 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: 464 Length of database: 475 Length adjustment: 33 Effective length of query: 431 Effective length of database: 442 Effective search space: 190502 Effective search space used: 190502 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