GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5404 in Caulobacter crescentus NA1000

Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate CCNA_01507 CCNA_01507 cystine transport system permease protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_5404
         (365 letters)



>FitnessBrowser__Caulo:CCNA_01507
          Length = 219

 Score =  103 bits (257), Expect = 4e-27
 Identities = 66/208 (31%), Positives = 109/208 (52%), Gaps = 6/208 (2%)

Query: 157 GLMLTLVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVM 216
           G   T+V++ +G+   + LG +LAL R S    +R     ++  +RG PL+  LF+    
Sbjct: 18  GAGYTIVLSVIGMSIGVVLGFLLALMRLSRSALLRWPAGVYVSAFRGTPLLVQLFLIYYG 77

Query: 217 LPLFLPEGMNFDKLLRALIGVILFQSAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMG 276
           LP F   G+    L+ A IG  L  +AY  E++R  + A+ KGQ+EAA+ +G+   +++ 
Sbjct: 78  LPQF---GLEMPPLVAAGIGFSLNVAAYSCEILRSAIAAVDKGQWEAASVLGMSRGQTLR 134

Query: 277 LVILPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNSVKQAAADPKWLGMATEGYVF 336
            VILPQA +  +  + N+FI+L KDTSL   I + +L    +   A    +      Y+ 
Sbjct: 135 RVILPQAARTAVAPLSNSFISLVKDTSLAATIQVPELFRQAQLITARTYEIFTL---YLA 191

Query: 337 AALVFWIFCFGMSRYSMHLERKLDTGHK 364
           AA ++WI    ++     LER+   G +
Sbjct: 192 AAAIYWILSTILAAAQTRLERRAAEGRR 219


Lambda     K      H
   0.330    0.144    0.469 

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: 253
Number of extensions: 11
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: 365
Length of database: 219
Length adjustment: 26
Effective length of query: 339
Effective length of database: 193
Effective search space:    65427
Effective search space used:    65427
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 47 (22.7 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