GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimD in Caulobacter crescentus NA1000

Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate CCNA_02128 CCNA_02128 acyl-CoA dehydrogenase

Query= metacyc::MONOMER-20676
         (396 letters)



>FitnessBrowser__Caulo:CCNA_02128
          Length = 401

 Score =  271 bits (693), Expect = 2e-77
 Identities = 168/399 (42%), Positives = 228/399 (57%), Gaps = 25/399 (6%)

Query: 11  AFRDEVRQFFKDNVPAKTRQKLIE------GRHNT--KEEMVEWYRILNKKGWAVTHWPK 62
           AFR + R + + N P      + E      GR       +   W   + ++GW    WPK
Sbjct: 11  AFRADTRAWLEANYPKSLNAPMGEDEAPWGGRKMVWKNPDAKLWLDRMAERGWTAPMWPK 70

Query: 63  EYGGTGWSSVQHYIFNEELQAAPA-PQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANVD 121
           EYGG G S  Q+ +  +EL+   A P  ++FGV M+GPV+  + +EEQK+RFLP I   +
Sbjct: 71  EYGGGGLSKAQNKVLEQELRRLKARPALMSFGVWMLGPVLLEYATEEQKQRFLPAIVRGE 130

Query: 122 DWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAKK 181
             WCQG+SEPG+GSDLASL+TK E KGD ++INGQK WT+ A  ADWIFCL RTD  +KK
Sbjct: 131 TRWCQGYSEPGAGSDLASLQTKCEDKGDHYLINGQKVWTSYADQADWIFCLVRTD-TSKK 189

Query: 182 QEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAKFLL 241
            EGISF+L DM + G+  RPI+ I G     E FFD+V+VP E LVG+ N GWD AK LL
Sbjct: 190 HEGISFVLFDMTSPGVEARPIKLISGSSPFCETFFDNVKVPKEQLVGKLNGGWDIAKRLL 249

Query: 242 GNERTGIARVGMSKERIRRIKQLAAQ---VESGGKPVIEDPKFRDKLAAVEIELKALELT 298
             ER  I+  G        + + A +   V+S G+  I D  FR +LAA  ++  A  LT
Sbjct: 250 QYERQNISASGFGGGGGLSVVEAAKKELGVDSEGR--IADGDFRARLAAHSMDAHAFMLT 307

Query: 299 QLRVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPYDVHGDDDSNET 358
             R  A E K G G P+ A S++K   +++ Q  TELL+E +G     +   G+D S E 
Sbjct: 308 VRRAEA-ESKQGSG-PSAAVSIIKYAAAKMNQERTELLVEALGLQGLGWS--GEDFSAEE 363

Query: 359 MDWTAQIAP-GYFNNRKVSIYGGSNEIQRNIICKAVLGL 396
           +      AP      +  SI GG++E+  N++ K VLGL
Sbjct: 364 L-----AAPRAMLRAKGNSIEGGTSEVNLNVVAKRVLGL 397


Lambda     K      H
   0.317    0.135    0.411 

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: 435
Number of extensions: 28
Number of successful extensions: 5
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: 396
Length of database: 401
Length adjustment: 31
Effective length of query: 365
Effective length of database: 370
Effective search space:   135050
Effective search space used:   135050
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 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