GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Shewanella sp. ANA-3

Align 3-hydroxy-3-methylglutaryl-coenzyme A lyase/3-methylglutaconyl-coenzyme A hydratase; EC 4.1.3.4; EC 4.2.1.18 (characterized)
to candidate 7024490 Shewana3_1668 hydroxymethylglutaryl-CoA lyase (RefSeq)

Query= CharProtDB::CH_122457
         (599 letters)



>FitnessBrowser__ANA3:7024490
          Length = 310

 Score =  259 bits (663), Expect = 9e-74
 Identities = 139/300 (46%), Positives = 194/300 (64%), Gaps = 7/300 (2%)

Query: 4   STKTVRIVEVGPRDGLQNIPQSIDSTIKLDLIRRLRDAGLQTIELTSFVSPRAIPQLADA 63
           S+  V + E+GPRDGLQN   ++ +  K+ LI  L DAG++ IE  SFVSP+ +PQ+AD+
Sbjct: 12  SSDRVSLFEMGPRDGLQN-EAAVPTQAKVALIESLADAGVKRIEAGSFVSPKWVPQMADS 70

Query: 64  QVVVQNADIQKLLKNPKLRLPVLVPNLKGLERALHNGIKEVAVFISATEGFSRANINCTV 123
             V     ++++ +   +    L PN+KGLE AL     EVA+F +A++ FS+ NINC++
Sbjct: 71  GDV-----LRQIRRQAGVVYSALTPNVKGLELALDAKASEVAIFGAASQSFSQRNINCSI 125

Query: 124 DEGLERARQVASRAASAGLSVRGYVSCIFADPYDGPTRPSSVLRCTKALLDAGCYEVSLG 183
           +E +ER   +   A +A + VRGYVSC+   PY+G    S V R ++ L   GCYE+SLG
Sbjct: 126 EESIERFIPLMDMAKAANIPVRGYVSCVLGCPYEGEIAASEVARVSEILYKMGCYEISLG 185

Query: 184 DTLGIGTPADVRWLITYLQDNGVPLEMLAGHFHDTYGGAVANVWEAYKCGLRMFDSSVAG 243
           DT+G+GTP   R ++  + +  VP+EMLA HFHDTYG A+AN+      G+R FD+SVAG
Sbjct: 186 DTIGVGTPLKARKMLQAVMER-VPVEMLALHFHDTYGQALANITACLDLGVRSFDASVAG 244

Query: 244 LGGCPXALGAKGNVASEDLVYMFERSGIHTGVDLSKLVETGEWISRQLSIAISSRAGAAL 303
           LGGCP A GA GN+ASEDLVYM    G+ TG+DL KL   G  IS+QL+    S+   A+
Sbjct: 245 LGGCPYAKGASGNLASEDLVYMLHGLGLKTGIDLEKLALAGFGISKQLNRLNGSKVANAI 304


Lambda     K      H
   0.318    0.134    0.389 

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: 407
Number of extensions: 18
Number of successful extensions: 4
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: 599
Length of database: 310
Length adjustment: 32
Effective length of query: 567
Effective length of database: 278
Effective search space:   157626
Effective search space used:   157626
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 (21.7 bits)
S2: 51 (24.3 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