GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-transport in Pseudomonas fluorescens FW300-N1B4

Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate Pf1N1B4_4622 Nitrate/nitrite transporter

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4622
          Length = 440

 Score =  324 bits (830), Expect = 4e-93
 Identities = 179/440 (40%), Positives = 255/440 (57%), Gaps = 14/440 (3%)

Query: 12  TQLQRTHKKIYRHLMPLLIVAYIISFIDRTNIGMAKATMSVDIGLSATAFGLGAGLFFLT 71
           +Q  R  ++I   L+P LI+ Y+I+++DR+ +G AK  M  DIGL   A+GLGAGLFF+ 
Sbjct: 2   SQELRLIRRITLKLIPFLILLYLIAYVDRSAVGFAKLHMGADIGLGDAAYGLGAGLFFIG 61

Query: 72  YAVLEIPSNLFLTRIGARRWIARIMITWGIISCGMAFVTGPTSFYVMRLLLGAAEAGLYP 131
           Y +LEIPSNL L R GARRW ARIM+TWG I+ GMAFV GP SFYVMR LLGAAEAG +P
Sbjct: 62  YFLLEIPSNLMLDRFGARRWFARIMVTWGAITIGMAFVQGPNSFYVMRFLLGAAEAGFFP 121

Query: 132 GIIYYLTLWFGREERAKATGLFLLGVCLANIIGAPLGGLLLSLDGMSGWHGWQWMFFIEG 191
           G++YY+T WF    R K  GLF+L   +A +I  P+ G LL +DG+ G HGWQW+F + G
Sbjct: 122 GVLYYITQWFPIRHRGKILGLFILSQPIAMMITGPVSGGLLGMDGIFGLHGWQWLFIVIG 181

Query: 192 LPAIALAFVVWRRLPDKPADARWLDSHDVQAITAVLEKEAE---ETRHTPSRFSLKTALT 248
           +PAI L + V R LPD P   +W+D  +   +T  L+K+ E   +TRH     +LK    
Sbjct: 182 MPAILLTWPVLRYLPDGPQQVKWMDQSEKDWLTGELKKDLEVYGQTRHGNPLHALK---- 237

Query: 249 TRVFLLLVLIYFTHQFSVYGLSYFLPGIIGSWGQLTPLQIGLLTAIPWIAAAAGGILLPR 308
            +  LLL L Y     S+YGL  +LP +I  +G  T L  G ++++P+I    G +++PR
Sbjct: 238 DKRVLLLALFYLPVTLSIYGLGLWLPTLIKQFGG-TDLVTGFVSSVPYIFGIIGLLIIPR 296

Query: 309 FARTEQRSRSMLMAGYLVMATGMAIGA-IAGHGVALLGFSLAAFMFFAMQSIIFNWLPSI 367
            +         L   Y++ A G+ + A +    + L    L AF  F+  ++ +      
Sbjct: 297 SSDRLNDRYGHLAVLYVLGAIGLFLSAWLTVPVLQLAALCLVAFALFSCTAVFWTLPGRF 356

Query: 368 MSGHMLAGSFGLLNCLGLCGGFLGPFILGAFEDRTGAATSGLWF-----AVALLIVGALA 422
            +G   A    L+N +G  GG++GPF++GA ++ TG   SGL+F        L++ G + 
Sbjct: 357 FAGASAAAGIALINSVGNLGGYIGPFVIGALKEYTGNLASGLYFLSCVMVFGLVLTGVVY 416

Query: 423 SLLIKSSSSSTPASAKQARG 442
            LL +         A  ARG
Sbjct: 417 RLLERKHVLPADQFAASARG 436


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: 562
Number of extensions: 25
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: 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