GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AO353_03045 in Caulobacter crescentus NA1000

Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate CCNA_01507 CCNA_01507 cystine transport system permease protein

Query= reanno::pseudo1_N1B4:Pf1N1B4_3433
         (232 letters)



>lcl|FitnessBrowser__Caulo:CCNA_01507 CCNA_01507 cystine transport
           system permease protein
          Length = 219

 Score =  123 bits (308), Expect = 3e-33
 Identities = 71/217 (32%), Positives = 117/217 (53%), Gaps = 9/217 (4%)

Query: 6   NVIWEALPLYLGGLVTTLKLLALSLFFGLLAALPLGLMRVSKQPVVNMSAWLFTYVIRGT 65
           +++ ++ PL L G   T+ L  + +  G++    L LMR+S+  ++   A ++    RGT
Sbjct: 6   DLLRQSAPLLLKGAGYTIVLSVIGMSIGVVLGFLLALMRLSRSALLRWPAGVYVSAFRGT 65

Query: 66  PMLVQLFLIYYGLAQFEAVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRATPN 125
           P+LVQLFLIYYGL QF       +          A + F++N +AY+ EI+  ++ A   
Sbjct: 66  PLLVQLFLIYYGLPQFGLEMPPLV---------AAGIGFSLNVAAYSCEILRSAIAAVDK 116

Query: 126 GEIEAAKAMGMSRIKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAAR 185
           G+ EAA  +GMSR +  +R++LP A R A+   SN  I +++ TSLA+ + + ++   A+
Sbjct: 117 GQWEAASVLGMSRGQTLRRVILPQAARTAVAPLSNSFISLVKDTSLAATIQVPELFRQAQ 176

Query: 186 TVNAQFYLPFEAYITAGVFYLCLTFILVRLFKMAEHR 222
            + A+ Y  F  Y+ A   Y  L+ IL       E R
Sbjct: 177 LITARTYEIFTLYLAAAAIYWILSTILAAAQTRLERR 213


Lambda     K      H
   0.330    0.140    0.427 

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: 95
Number of extensions: 3
Number of successful extensions: 2
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: 232
Length of database: 219
Length adjustment: 22
Effective length of query: 210
Effective length of database: 197
Effective search space:    41370
Effective search space used:    41370
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: 46 (22.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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