GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Caulobacter crescentus NA1000

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate CCNA_01648 CCNA_01648 adenosylmethionine-8-amino-7-oxononanoate

Query= reanno::BFirm:BPHYT_RS23155
         (482 letters)



>FitnessBrowser__Caulo:CCNA_01648
          Length = 420

 Score =  139 bits (349), Expect = 2e-37
 Identities = 97/312 (31%), Positives = 146/312 (46%), Gaps = 21/312 (6%)

Query: 61  IVKAQGVYLWDSEGNKVIDGMAGLWCVNVGYGRKELADAAYKQMQELPYYNTFFKTTHPP 120
           +V  +G  L   +G +++DG+A  W    GY    +A A  KQ++ +P+   F    H P
Sbjct: 30  VVATRGARLILEDGRELVDGLASWWTACHGYNHPHIAGALRKQIETMPHV-MFGGLAHEP 88

Query: 121 VIELSALLAELAPEAFNHFFYCNSGSEGNDTVLRIVHQYWATQGKHSKKFVISRKNGYHG 180
              L+  LA L P   +H F+  SGS   +  +++  QY   +G   +   ++ + GYHG
Sbjct: 89  AYRLAKRLARLLPGDLDHVFFAESGSVAVEIAMKMALQYQINRGVGGRTRFLAFRGGYHG 148

Query: 181 STIAGGTL-GGMGYMHEQMPSKVENIVHIDQPYFFGEAQGNLTPEEFALARAQQLEAKIL 239
            T+A  T+      MH      +   V  D P           P   A   A      +L
Sbjct: 149 DTLATMTVCDPEEGMHSLFAGVMPAQVIADLP---------RDPASEAALDA------LL 193

Query: 240 EIGADNVAAFIGEP-FQGAGGVIFPASTYWPEIQRICRKYDILLVADEVIGGFGRTGEWF 298
                 +AA + EP  QGAGG++         ++R+  K+ +LL+ DE+  GFGRTG  F
Sbjct: 194 AARGHEIAAMLVEPLIQGAGGMLPHPPEVLRTLRRLADKHGVLLIFDEIFTGFGRTGSLF 253

Query: 299 AHQHFGFEPDLITLAKGLTSGYVPMGAVGLHDRVAKAIIEN---GDFNHGLTYSGHPVAA 355
           A Q  G EPD++TL+K LT G +P+ A      V +A   +       HG TY  +P+A 
Sbjct: 254 AMQAAGVEPDIVTLSKALTGGTLPLSAAVARRHVFEAFWSDDPAAALMHGPTYMANPLAC 313

Query: 356 AVAVANLKLLRD 367
           A A A+L L  D
Sbjct: 314 AAANASLDLFED 325


Lambda     K      H
   0.319    0.136    0.408 

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: 466
Number of extensions: 20
Number of successful extensions: 4
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: 482
Length of database: 420
Length adjustment: 33
Effective length of query: 449
Effective length of database: 387
Effective search space:   173763
Effective search space used:   173763
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: 51 (24.3 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