GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bch in Caulobacter crescentus NA1000

Align 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial; 3-hydroxyisobutyryl-coenzyme A hydrolase; HIB-CoA hydrolase; HIBYL-CoA-H; EC 3.1.2.4 (characterized)
to candidate CCNA_01414 CCNA_01414 3-hydroxyisobutyryl-CoA hydrolase

Query= SwissProt::Q5XIE6
         (385 letters)



>FitnessBrowser__Caulo:CCNA_01414
          Length = 350

 Score =  272 bits (696), Expect = 9e-78
 Identities = 147/348 (42%), Positives = 213/348 (61%), Gaps = 10/348 (2%)

Query: 32  TETAEVLLERRGCAGVITLNRPKLLNALSLNMIRQIYPQLKKWERDPDTFLIIIKGAGGK 91
           T+  EVL+      G ITLNRPK L+AL+L M   +   L  W+ DP+ ++++I   G +
Sbjct: 2   TDDPEVLIRVEKNVGRITLNRPKALHALTLGMCETMIGALLDWQDDPEVYMVLIDHTGER 61

Query: 92  AFCAGGDIKALSEAKKAGQTLSQDLFREEYILNNAIASCQKPYVALIDGITMGGGVGLSV 151
            FCAGGDI+ L+++       ++  F  EY LN+ + + + P VA++DGI MGGGVG+S+
Sbjct: 62  GFCAGGDIRMLADSGAKDGVEARRFFHTEYQLNHLLFTYETPVVAVMDGIVMGGGVGISM 121

Query: 152 HGQFRVATERSLFAMPETGIGLFPDVGGGYFLPRLQGKLGYFLALTGFRLKGRDVHRAGI 211
               R+ATER+ FAMPETGIGLFPDVGGG++LPRL GK G +LALTG R+KG D  R GI
Sbjct: 122 PAHIRIATERTTFAMPETGIGLFPDVGGGWYLPRLPGKAGLWLALTGARIKGADCMRLGI 181

Query: 212 ATHFVDSEKLHVLEEELLALKSPSAEDVAGVLESYHAKSKMGQDKSIIFEEHMDKINSCF 271
           ATHFV+   +  L++ ++A        +   L  Y A +  G+   + FE+ ++++   F
Sbjct: 182 ATHFVEFGAVEGLKKAIIA----DPRRIEETLRKYRADA--GKASLLGFEQDLNRL---F 232

Query: 272 SANTVEQILENLRQDGSPFAMEQIKVINKMSPTSLKITLRQLMEGST-KTLQEVLTMEYR 330
              +VE+I E L  D S +   Q++V+   SP +LK+   QL  G+  +   + + MEYR
Sbjct: 233 VGESVEEIFEFLTLDSSDWGKAQLEVMKTKSPQTLKVAFEQLKRGAAMEDFADNMAMEYR 292

Query: 331 LTQACMEGHDFHEGVRAVLIDKDQTPKWKPADLKDVTDEDLNSYFKSL 378
           +    +  HDF EGVRAV++DKD  P+W PA ++DVTD  L   F  L
Sbjct: 293 IGSRVVMKHDFIEGVRAVIVDKDNAPRWSPARVEDVTDAALAEIFAPL 340


Lambda     K      H
   0.320    0.136    0.394 

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: 304
Number of extensions: 14
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: 385
Length of database: 350
Length adjustment: 30
Effective length of query: 355
Effective length of database: 320
Effective search space:   113600
Effective search space used:   113600
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