GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaE in Cupriavidus basilensis 4G11

Align 1,2-phenylacetyl-CoA epoxidase, subunit E; 1,2-phenylacetyl-CoA epoxidase, reductase subunit; 1,2-phenylacetyl-CoA monooxygenase, subunit E; EC 1.-.-.- (characterized)
to candidate RR42_RS31980 RR42_RS31980 3-ketosteroid-9-alpha-hydroxylase

Query= SwissProt::P76081
         (356 letters)



>FitnessBrowser__Cup4G11:RR42_RS31980
          Length = 342

 Score =  191 bits (484), Expect = 3e-53
 Identities = 120/351 (34%), Positives = 184/351 (52%), Gaps = 20/351 (5%)

Query: 4   FHSLTVAKVESETRDAVTITFAVPQPLQEAYRFRPGQHLTLKASFDGEELRRCYSICRS- 62
           FH L +A+V +ET +A ++ F +P  L++ + +RPGQ LTLK   +G   +RCYS+  S 
Sbjct: 6   FHPLRIAQVVAETDEASSLVFELPDGLRDTFAYRPGQFLTLKVPLEGAAQQRCYSLSSSP 65

Query: 63  YLPGEISVAVKAIEGGRFSRYAREHIRQGMTLEVMVPQGHFGYQPQAERQGRYLAIAAGS 122
            +   + V +K + GGR S +  + +  G T+EVM P G F         G  L  A GS
Sbjct: 66  QVDSALRVTIKRVRGGRVSNWICDRLGAGDTVEVMPPAGVF---TPRSLDGDLLLFAGGS 122

Query: 123 GITPMLAIIATTLQTEPESQFTLIYGNRTSQSMMFRQALADLKDKYPQRLQLLCIFSQET 182
           GITP+L+I    L+       TLIY NR  +S++FR AL +L  ++  RL+++       
Sbjct: 123 GITPVLSIAKAALR-HGGGNVTLIYANRDERSVIFRDALCELAARHADRLRVI-----HW 176

Query: 183 LDSDLLHGRIDGEKLQSLGASLINFRLYDEAFICGPAAMMDDAETALKALGMPDKTIHLE 242
           LDS  + G     +L++L A       + + FICGP   MD A+ AL+ LG+  + IH+E
Sbjct: 177 LDS--VQGPPSQAQLEALAAPWG----HADCFICGPGPFMDGAQAALQTLGVARERIHVE 230

Query: 243 RFNTP---GTRVKRSVNVQSDGQKVTVRQDGRDREIVLNADDESILDAALRQGADLPYAC 299
           RF  P       K           + V  DG    +  +A  E++LDA LR G   P +C
Sbjct: 231 RFGAPPPAAVPAKEQTPAACAPAALEVELDGVRHRLDAHAG-ETVLDAMLRAGVAAPNSC 289

Query: 300 KGGVCATCKCKVLRGKVAMETNYSLEPDELAAGYVLSCQALPLTSDVVVDF 350
           + G+C  C C+V  G+  +  N+ L+  +  AG+ L+CQA    S++ + F
Sbjct: 290 RSGLCGACMCQVTHGEATLGENHVLDAADREAGWTLACQARAAGSELHLKF 340


Lambda     K      H
   0.320    0.135    0.390 

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: 309
Number of extensions: 20
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: 356
Length of database: 342
Length adjustment: 29
Effective length of query: 327
Effective length of database: 313
Effective search space:   102351
Effective search space used:   102351
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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