GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaE in Sinorhizobium meliloti 1021

Align ring 1,2-phenylacetyl-CoA epoxidase PaaE subunit (EC 1.14.13.149) (characterized)
to candidate SM_b21636 SM_b21636 ferredoxin reductase electron transfer protein

Query= metacyc::MONOMER-15950
         (357 letters)



>FitnessBrowser__Smeli:SM_b21636
          Length = 358

 Score =  354 bits (909), Expect = e-102
 Identities = 181/360 (50%), Positives = 248/360 (68%), Gaps = 6/360 (1%)

Query: 1   MSKFHSLTIKEVRPETRDAVSIAFDVPAELADSFRFTQGQHLVMRTQLDGEEVRRSYSIC 60
           M++F+ L + EVR +TRDAV +  +   E   +F FTQGQ+L  R    GEE+RRSYSIC
Sbjct: 1   MARFYPLQVTEVRRDTRDAVVVTLEPREEDRAAFDFTQGQYLTFRRLFGGEELRRSYSIC 60

Query: 61  TGVNDGELRVAIKRVAGGRFSAYANESLKAGQRLEVMPPSGHFH--VELDAARHGNYLAV 118
            G+++G L+V IKRV  G FS++ANE L+ G  LE MPP G F   +E +AA+H  YL  
Sbjct: 61  AGLDEGALKVGIKRVDDGCFSSWANEELEPGDTLEAMPPMGAFFTPIEPEAAKH--YLGF 118

Query: 119 AAGSGITPILSIIKTTLETEPHSRVTLLYGNRSSASTLFREQLEDLKNRYLQRLNLIFLF 178
           A GSGITP+LS++KT L  EP S  TL+Y NR  +S +FRE+L+DLKN YL RL+++ + 
Sbjct: 119 AGGSGITPVLSLVKTVLAREPRSAFTLVYANRHFSSIMFREELDDLKNLYLGRLSVLHVL 178

Query: 179 SREQQDVDLYNGRIDADKCGQLFSRWIDVKALDAAFICGPQAMTETVRDQLKANGMAAER 238
             E Q++DL++GR+D +KC  LF  WIDV++ D AFICGP+ M   V   L+A+G+  +R
Sbjct: 179 ESEAQEIDLFSGRLDREKCTALFRSWIDVRSADTAFICGPEPMMLGVAAALRAHGLGDDR 238

Query: 239 IHFELFAAAGSAQKREARESAAQDSSVS--QITVISDGRELSFELPRNSQSILDAGNAQG 296
           I FELFAA+   + R   ESAA   S +  + TV  DG   SF  P+   S+L+A     
Sbjct: 239 IKFELFAASQPGRARRKVESAAGADSRARCEATVTLDGATRSFTFPKEGLSLLEAALENR 298

Query: 297 AELPYSCKAGVCSTCKCKVVEGEVEMDSNFALEDYEVAAGYVLSCQTFPISDKVVLDFDQ 356
            + P++CKAGVCS+C+ KV+EGEVEM+SN ALEDYEV  GYVL+CQ++P+SD++V+ +DQ
Sbjct: 299 MDAPFACKAGVCSSCRAKVLEGEVEMESNNALEDYEVEQGYVLTCQSYPLSDRIVVSYDQ 358


Lambda     K      H
   0.319    0.133    0.377 

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: 357
Number of extensions: 16
Number of successful extensions: 2
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: 357
Length of database: 358
Length adjustment: 29
Effective length of query: 328
Effective length of database: 329
Effective search space:   107912
Effective search space used:   107912
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.

Links

Downloads

Related tools

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