GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bch in Rhodococcus qingshengii djl-6-2

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 WP_050655249.1 C1M55_RS19620 enoyl-CoA hydratase/isomerase family protein

Query= SwissProt::Q5XIE6
         (385 letters)



>NCBI__GCF_002893965.1:WP_050655249.1
          Length = 352

 Score =  283 bits (723), Expect = 7e-81
 Identities = 154/353 (43%), Positives = 215/353 (60%), Gaps = 12/353 (3%)

Query: 32  TETAEVLLERRGCAGVITLNRPKLLNALSLNMIRQIYPQLKKWERDPDTFLIIIKGAGGK 91
           ++  EVL+E+R   G+ITLNRPK +NAL+ +M++ +   L +W+ D D   +++ GAG +
Sbjct: 2   SDELEVLIEKRDGLGLITLNRPKAINALNHSMVKAMAKALAEWKYDDDVKAVVLTGAGER 61

Query: 92  AFCAGGDIKALSEAKKAGQTLSQDLFREEYILNNAIASCQKPYVALIDGITMGGGVGLSV 151
             CAGGDI ++    K G+T S D +REEYILN+ IA+  KPYVA++DGI MGGGVG+S 
Sbjct: 62  GLCAGGDIVSIYHDAKDGKTGSLDFWREEYILNSEIANYPKPYVAIMDGIVMGGGVGVSA 121

Query: 152 HGQFRVATERSLFAMPETGIGLFPDVGGGYFLPRLQGKLGYFLALTGFRLKGRDVHRAGI 211
           HG  R+ TERS+  MPETGIG  PDVGG Y L R  G+LG  +ALT  RL   D   AG 
Sbjct: 122 HGDIRIVTERSMIGMPETGIGFIPDVGGTYLLSRAPGELGTHIALTTARLSAGDAIAAGF 181

Query: 212 ATHFVDSEKLHVLEEELLALKSPSAEDVAGVLESYHAKSKMGQDKSIIFEEHMDKINSCF 271
           A HF+ SE    +E  + AL S S  D           S++   +S         I++ +
Sbjct: 182 ADHFIPSEN---IETFIAALASSSVADAVAQYAEPAPVSELSAQQS--------WIDAAY 230

Query: 272 SANTVEQILENLRQDGSPFAMEQIKVINKMSPTSLKITLRQLMEG-STKTLQEVLTMEYR 330
           SA+ V  I+E LR  G P A +  + I   SP +L +TLR L       +L+EVL  E+R
Sbjct: 231 SADDVSTIVERLRASGIPEAEKAAEQILGKSPIALSVTLRSLRHAKEAASLEEVLNEEFR 290

Query: 331 LTQACMEGHDFHEGVRAVLIDKDQTPKWKPADLKDVTDEDLNSYFKSLGSRDL 383
           ++ A +  HD  EG+RA +++KD+ PKW PA L+DVT E +++YF  LG  +L
Sbjct: 291 VSTAALASHDLVEGIRAQVVEKDRNPKWLPATLEDVTAESVDAYFAPLGDNEL 343


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: 297
Number of extensions: 8
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: 352
Length adjustment: 30
Effective length of query: 355
Effective length of database: 322
Effective search space:   114310
Effective search space used:   114310
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 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