GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruE in Phyllobacterium brassicacearum STM 196

Align Fructose import binding protein FruE (characterized)
to candidate WP_106712861.1 CU102_RS19525 ABC transporter substrate-binding protein

Query= SwissProt::Q8G848
         (327 letters)



>NCBI__GCF_003010955.1:WP_106712861.1
          Length = 318

 Score =  122 bits (307), Expect = 9e-33
 Identities = 96/305 (31%), Positives = 150/305 (49%), Gaps = 14/305 (4%)

Query: 17  LVSVAACGSSNAGGSSDSGKKTVGFVAVGPEGGFRTANEKDIQKAFEDAGFDLTYSPTQN 76
           L S  A   + A  +SD    TVGF  +G E G+R A     +   +    DL  +  Q 
Sbjct: 6   LASTVAMSFAGAASASDL---TVGFSQIGSESGWRAAETSVSKIEAKKRSIDLKIADAQQ 62

Query: 77  NDQQKQIQAFNKFVNDEVDAIILSSTEDSGWDDSLKKAAEAEIPVFTVDRNVDVKDAEAK 136
             Q+ QI+A   FV   VDAI ++    +GWD  L +A EAEIPV  +DR ++  + +  
Sbjct: 63  K-QENQIKAIRGFVAQGVDAIFVAPVVATGWDTVLAEAKEAEIPVILLDRTIETANND-- 119

Query: 137 KAIVAHIGPSNVWCGEQAAEFVNKNFP-DGANGFILEGPAGLSVVKDRGTGW--GNKVAS 193
              +  +    V  G+ A +++ K       N   L+G  G S   +R  G+  G   AS
Sbjct: 120 -LYLTAVTSDTVHEGKVAGDWLVKTTAGKPCNVVELQGTVGSSPAINRKKGFEEGIASAS 178

Query: 194 NVKVLESQSANWSTDEAKTVTAGLLD-KYKSDNPQFIFAQNDEMGLGAAQAVDAAGLK-G 251
           N+K+  SQ+ +++  + K V  G L  +    N   ++A ND+M +GA QA+  AGLK G
Sbjct: 179 NIKITRSQTGDFTRAKGKEVMEGFLKAENGGKNICALYAHNDDMAVGAIQAIKEAGLKPG 238

Query: 252 K-VKIITIDGTKNALQALVDGDLSYVIEYNPIFGKETAQAVKDYLD-GKTVEKDIEIESK 309
           K + +++ID   +  +A+ +G+ +  +E  P        A+K Y D GK   K I+ ESK
Sbjct: 239 KDILVVSIDAVPDIFKAMSEGEANATVELTPNMAGPAFDALKAYKDSGKAPPKWIQTESK 298

Query: 310 TFDAA 314
            +  A
Sbjct: 299 LYTQA 303


Lambda     K      H
   0.310    0.128    0.360 

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: 234
Number of extensions: 14
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: 327
Length of database: 318
Length adjustment: 28
Effective length of query: 299
Effective length of database: 290
Effective search space:    86710
Effective search space used:    86710
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 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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