GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-transport in Pseudomonas putida KT2440

Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate PP_3176 PP_3176 Major facilitator family transporter

Query= reanno::Koxy:BWI76_RS23715
         (445 letters)



>FitnessBrowser__Putida:PP_3176
          Length = 440

 Score =  270 bits (689), Expect = 9e-77
 Identities = 154/433 (35%), Positives = 235/433 (54%), Gaps = 9/433 (2%)

Query: 11  GTQLQRT--HKKIYRHLMPLLIVAYIISFIDRTNIGMAKATMSVDIGLSATAFGLGAGLF 68
           GT   R   +++I   L+P + + Y+ +++DR N+G AK  M   +  S T +GLGAG+F
Sbjct: 10  GTDTTRNALYRRITLRLIPFIFICYLFNYLDRVNVGFAKLQMLDALKFSETVYGLGAGIF 69

Query: 69  FLTYAVLEIPSNLFLTRIGARRWIARIMITWGIISCGMAFVTGPTSFYVMRLLLGAAEAG 128
           F+ Y +  +PSNL L R G RRWIA +MI WG +S  + FVT PT FY +RLL GAAEAG
Sbjct: 70  FIGYVLCGLPSNLALNRFGPRRWIALMMIAWGSLSTCLLFVTTPTEFYTLRLLTGAAEAG 129

Query: 129 LYPGIIYYLTLWFGREERAKATGLFLLGVCLANIIGAPLGGLLLS--LDGMSGWHGWQWM 186
            +PG++ YL+ WF    R +   LF+  + ++ ++G P  G +L     G  G  GWQWM
Sbjct: 130 FFPGVVLYLSRWFPAARRGRIMALFMSAIPVSGLLGGPFSGWILEHFAAGQHGLAGWQWM 189

Query: 187 FFIEGLPAIALAFVVWRRLPDKPADARWLDSHDVQAITAVLEKEAEETRHTPSRFSLKTA 246
           F I+GLP +AL  +    L D    A WL   + Q I A L+ +A     T S  S+   
Sbjct: 190 FLIQGLPTVALGVLAVFLLSDGYQKAAWLSPAERQLIAADLQADAASKPSTTSD-SVLAV 248

Query: 247 LTTRVFLLLVLIYFTHQFSVYGLSYFLPGIIGSWGQLTPLQIGLLTAIPWIAAAAGGILL 306
           LT  +      +YF  Q  VY ++++LP II  +    PL IG L+AIP++ A    IL 
Sbjct: 249 LTNPLIWTFGFVYFCIQSGVYAINFWLPSIIKGFD--NPLLIGWLSAIPYLLAGVFMILC 306

Query: 307 PRFARTEQRSRSMLMAGYLVMATGMAIGA-IAGH-GVALLGFSLAAFMFFAMQSIIFNWL 364
            R A      R  L+   L+ A G+ I    AG+  +A+LG S+A         + +   
Sbjct: 307 GRSADLRNERRWHLVVPMLMGAVGLLIAVNFAGNPTIAILGLSIATMGALTGLPMFWPMP 366

Query: 365 PSIMSGHMLAGSFGLLNCLGLCGGFLGPFILGAFEDRTGAATSGLWFAVALLIVGALASL 424
            +++S         ++N +G   GFL P+++G  +D+TG+  + L+   AL+++G+L +L
Sbjct: 367 TALLSAGAAVAGLAIINSVGQMAGFLSPYLVGFIKDQTGSTDAALYSLAALIVLGSLVAL 426

Query: 425 LIKSSSSSTPASA 437
            +  + S + A A
Sbjct: 427 RVTRAGSLSTARA 439


Lambda     K      H
   0.328    0.141    0.438 

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: 482
Number of extensions: 20
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: 445
Length of database: 440
Length adjustment: 32
Effective length of query: 413
Effective length of database: 408
Effective search space:   168504
Effective search space used:   168504
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 (21.7 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