GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Caulobacter crescentus NA1000

Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate CCNA_02178 CCNA_02178 short-chain alcohol dehydrogenase

Query= SwissProt::Q9NKW1
         (441 letters)



>FitnessBrowser__Caulo:CCNA_02178
          Length = 301

 Score =  281 bits (718), Expect = 3e-80
 Identities = 140/277 (50%), Positives = 199/277 (71%), Gaps = 6/277 (2%)

Query: 3   LNFKDKVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKA 62
           + F  KV IVTGAGGG+G+ +ALE A+RGAKVVVNDLGGS  G G SS+AA KVV+EIKA
Sbjct: 4   IRFDGKVAIVTGAGGGLGRQHALELARRGAKVVVNDLGGSMDGSGGSSEAAQKVVDEIKA 63

Query: 63  AGGTAVANYDSVEDGEKI---VQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYR 119
            GG A+AN  SV D   +   ++ AMD++G +DILI NAGILRD +  KM   D++LV +
Sbjct: 64  LGGEAIANGSSVTDDAGVALMIKQAMDTWGRIDILIANAGILRDKTLTKMELADFELVMQ 123

Query: 120 VHAKGAYKLSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQE 179
           VH  G +K  +A W+ M+ +N+GRI++T+S++G+YGNFGQ+NYG+ KMA++GL NTL  E
Sbjct: 124 VHVFGTFKPIKAVWDIMKAQNYGRIVVTTSSSGMYGNFGQSNYGAAKMAVLGLMNTLKLE 183

Query: 180 GKSKNIHCNTIAPIAASRLTESVMPPEILEQMKPDYIVPLVLYLCHQDTTETGGVFEVGA 239
           G   ++  N I+P+AA+R+TE +MPPE+L ++ P+Y+ P V+YLC  D   TG +   GA
Sbjct: 184 GAKNDVKINAISPVAATRMTEGLMPPEVLAKLAPEYVTPGVVYLC-SDEAPTGAILTAGA 242

Query: 240 GWVSKVRLQRSAGVYMKD--LTPEKIKDNWAQIESFD 274
           G  +  R+  + GVY+ +  L+ E+++D+W QI + D
Sbjct: 243 GAFALSRIYETEGVYLGEGGLSAEEVRDSWGQITAED 279


Lambda     K      H
   0.313    0.131    0.371 

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: 394
Number of extensions: 26
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: 441
Length of database: 301
Length adjustment: 29
Effective length of query: 412
Effective length of database: 272
Effective search space:   112064
Effective search space used:   112064
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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