GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcE in Herbaspirillum seropedicae SmR1

Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate HSERO_RS19100 HSERO_RS19100 FAD-binding protein

Query= reanno::Cup4G11:RR42_RS17310
         (374 letters)



>FitnessBrowser__HerbieS:HSERO_RS19100
          Length = 359

 Score =  406 bits (1043), Expect = e-118
 Identities = 214/368 (58%), Positives = 262/368 (71%), Gaps = 16/368 (4%)

Query: 7   DQQATLTAFRDAIRHATGTRTPLRLRGGGSKDFYGQHPQGTLLDTRAYSGIVDYDPPELV 66
           D  A L +FR+ I        PL++RGGG+KD+YGQ P G LLDTRAYSGI+DY+P ELV
Sbjct: 8   DLDAVLASFRERILAGR----PLQIRGGGTKDWYGQTPSGELLDTRAYSGIIDYEPTELV 63

Query: 67  ITARCGTPLAQIEAALAERRQMLAFEPPHFSTGADGSDVATIGGAVAAGLSGPRRQAVGA 126
           ITARCGTPL++I+AALA+  QMLA+EPP F         AT+GG VAAGLSGP R + GA
Sbjct: 64  ITARCGTPLSEIDAALAQHNQMLAWEPPSFG------GAATVGGMVAAGLSGPARASAGA 117

Query: 127 LRDFVLGTRVMDGRGDVLSFGGQVMKNVAGYDVSRLMSGSLGTLGLILEVSLKVLPVPFD 186
           +RDFVLG  +MD +G+ L FGGQVMKNVAGYD+SRL++GSLGTLGLILEVSLKVLP P  
Sbjct: 118 VRDFVLGAVLMDAQGEPLHFGGQVMKNVAGYDISRLLAGSLGTLGLILEVSLKVLPRPIA 177

Query: 187 DATLRFALDEAAALDRLNDWGGQPLPIAASAWHDGVLHLRLSGAAAALRAARARLGGEAV 246
            +T  F +++  AL  LN   GQPLP+ ASAW   VL +RLSGA AA+ +A A+LGG   
Sbjct: 178 SSTRVFEINQEGALRLLNQSAGQPLPLVASAWVGNVLTIRLSGAQAAVDSAIAKLGG--T 235

Query: 247 DAAQADALWRALREHSHAFFAPVQAGRALWRIAVPTTAAPLALPGGQLIEWGGGQRWWLG 306
           + +  D  W  LRE +H FFA  +A   LWR+++P+ AAP+ LPG QLIEWGG QRW   
Sbjct: 236 ELSNPDDYWTDLREQTHPFFADAEA--PLWRLSLPSVAAPIDLPGRQLIEWGGAQRWL-- 291

Query: 307 GSDSAADSAIVRAAAKAAGGHATLFRNGDKAVGVFTPLSAPVAAIHQRLKATFDPAGIFN 366
             +   D+  +RAAA A GGHA+L R GDKA+GVF PL   V  +H+RLK  FDP GIFN
Sbjct: 292 RPEGNVDAVTIRAAALAVGGHASLHRGGDKAIGVFHPLQPAVETLHRRLKQQFDPQGIFN 351

Query: 367 PQRMYAGL 374
           P R+YA L
Sbjct: 352 PGRLYASL 359


Lambda     K      H
   0.321    0.136    0.414 

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: 444
Number of extensions: 20
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 374
Length of database: 359
Length adjustment: 30
Effective length of query: 344
Effective length of database: 329
Effective search space:   113176
Effective search space used:   113176
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