GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Caulo:CCNA_02178 CCNA_02178 short-chain alcohol
           dehydrogenase
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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