GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfQ in Paraburkholderia bryophila 376MFSha3.1

Align Galactofuranose-binding protein YtfQ (characterized)
to candidate H281DRAFT_05269 H281DRAFT_05269 monosaccharide ABC transporter substrate-binding protein, CUT2 family

Query= SwissProt::P39325
         (318 letters)



>FitnessBrowser__Burk376:H281DRAFT_05269
          Length = 328

 Score =  273 bits (698), Expect = 4e-78
 Identities = 151/322 (46%), Positives = 205/322 (63%), Gaps = 15/322 (4%)

Query: 4   RLLIVSAVSAAMSSMALAAP--------LTVGFSQVGSESGWRAAETNVAKSEAEKRGIT 55
           R L   A+ A   ++ LA P        +T+GF+QVG+ES WR A T   KS A    I 
Sbjct: 10  RALGALALCAGFGTLTLATPGAYAQDKQITLGFAQVGAESAWRTANTESVKSAAADAKIK 69

Query: 56  LKIADGQQKQENQIKAVRSFVAQGVDAIFIAPVVATGWEPVLKEAKDAEIPVFLLDRSID 115
           LK +D QQKQENQIKA+RS++AQ VD I  +PVV +GWEPVL+EAK A+IPV L DR++D
Sbjct: 70  LKFSDAQQKQENQIKAIRSYIAQKVDVIAFSPVVESGWEPVLREAKAAKIPVILTDRNVD 129

Query: 116 VKDKSLYMTTVTADNILEGKLIGDWLV---KEVNGKPCNVVELQGTVGASVAIDRKKGFA 172
           VKD SLY+T + +D + EG+  G WL    K+  G P N+ ELQGTVG++ A DR  G  
Sbjct: 130 VKDTSLYVTMIGSDFLEEGRRGGKWLADHYKDAQG-PVNIAELQGTVGSAPANDRHAGLI 188

Query: 173 EAIKNAPNIKIIRSQSGDFTRSKGKEVMESFIKAENNGKNICMVYAHNDDMVIGAIQAIK 232
           E IK+ P  K+I SQSGDFT + GK+VME+FIK   N  N+  VYAHNDDM +GAIQA++
Sbjct: 189 EVIKSDPKFKVIASQSGDFTLAGGKQVMEAFIKTYGNKINV--VYAHNDDMALGAIQAME 246

Query: 233 EAGLKPGKDILTGSIDGVPDIYKAMMDGEANASVELTPNMAGPAFDALEKYKKDGTMPEK 292
           EAG+ PGKD++  S D     ++AM  G+ N  VE +P +      A++       +P++
Sbjct: 247 EAGMHPGKDVIVVSFDATKGGFQAMAAGKMNVDVECSPLLGPQLMSAVKDVVAGKPLPKR 306

Query: 293 LTLTKSTLYLPDTAKEELEKKK 314
           + LT+ T++    A + L  +K
Sbjct: 307 I-LTEETVFPMSVAAQTLPTRK 327


Lambda     K      H
   0.313    0.130    0.363 

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: 268
Number of extensions: 9
Number of successful extensions: 3
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: 318
Length of database: 328
Length adjustment: 28
Effective length of query: 290
Effective length of database: 300
Effective search space:    87000
Effective search space used:    87000
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: 48 (23.1 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