GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Dokdonella koreensis DS-123

Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_067648668.1 I596_RS12940 enoyl-CoA hydratase

Query= reanno::BFirm:BPHYT_RS17335
         (258 letters)



>NCBI__GCF_001632775.1:WP_067648668.1
          Length = 260

 Score =  190 bits (483), Expect = 2e-53
 Identities = 113/263 (42%), Positives = 157/263 (59%), Gaps = 8/263 (3%)

Query: 1   MAYENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGS-EK 59
           MA+ N+L   RG V  +T+NRP  LNAL+   + EL  A  +   D+A+  +V+ G+ EK
Sbjct: 1   MAFRNLLSTDRGGVRTITINRPDKLNALDRQTIGELQIAFEQARHDEAVRVVVLAGAGEK 60

Query: 60  AFAAGADIGMMSTYTYMDVYK----GDYITRNWETVRSIRKPIIAAVAGFALGGGCELAM 115
           AF AGADI  ++T T +        G  + R  ET   + KP+IA + GFALGGG ELAM
Sbjct: 61  AFVAGADITELATLTPVQAQAFARAGQRMVRAIET---LGKPVIARLNGFALGGGLELAM 117

Query: 116 MCDIIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAG 175
            C +  A+  AK GQPEI LG++PG GGTQRL R   +A A++LCL    +DAA A + G
Sbjct: 118 ACHLRIASTRAKVGQPEINLGVIPGFGGTQRLARLAGRAAALELCLLGTPIDAARAYQLG 177

Query: 176 LVSRVIPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLF 235
           LV+RV+   +L +   A A  +A     A+  V ++V  A E  + EG+ +E + F   F
Sbjct: 178 LVNRVVEPEALDEAVQAVADQLAASAPQALAGVLDTVLAATELAIEEGLDYEAKAFSLCF 237

Query: 236 ATEDQKEGMAAFVEKRKPVFKHR 258
           +TED +EG AAF+ +RK VF  R
Sbjct: 238 STEDMREGTAAFLARRKAVFSGR 260


Lambda     K      H
   0.321    0.134    0.380 

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: 148
Number of extensions: 9
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: 258
Length of database: 260
Length adjustment: 24
Effective length of query: 234
Effective length of database: 236
Effective search space:    55224
Effective search space used:    55224
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 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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