GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutW in Pseudomonas fluorescens FW300-N2C3

Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate AO356_09245 AO356_09245 ABC transporter permease

Query= TCDB::Q9KKE2
         (285 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_09245
          Length = 283

 Score =  211 bits (538), Expect = 1e-59
 Identities = 109/263 (41%), Positives = 180/263 (68%), Gaps = 6/263 (2%)

Query: 12  APVNDFIQALVTNYGWVFKAISGVILKAVLFIEWILRGL-PWWLVILAFMALACRSSRRW 70
           APV D++ A   N   +F  IS V+   +  +E +L    P+ ++ + F+A    +++R 
Sbjct: 15  APVVDWLNA---NLHGLFVVISQVVEAVLGLVEHLLLAPHPYMMIAIVFVAAFIFATKRV 71

Query: 71  SLTLAVCALLETVGVLGIWDLTMQTLALMLMATIVSVVIGVPMGILVAKSRVVRNITLPV 130
           ++  A+  +L      G+W  +MQT+AL+ ++ ++SV I  P+G+L A+ + V +  LP+
Sbjct: 72  AVFAAL--MLAFCLFSGLWVASMQTIALVSVSVLISVAIAFPLGVLAARVKRVDDAFLPI 129

Query: 131 LDVMQTMPSFVYLIPALMLFGLGKVPAILATIIYAVPPLIRLTDLGIRQVDAEVVEAATA 190
           L++MQT+P +VYLIPA++LF LG+VPAI+ATI+Y +PP++RLT L  +Q+  +++E   A
Sbjct: 130 LNIMQTVPPWVYLIPAVILFSLGRVPAIIATIVYGIPPMLRLTTLAFKQLPKDLLELGQA 189

Query: 191 FGGSPGQILFGVELPLATPTIMAGLNQTIMMALSMVVVASMIGARGLGEQVLNGIQTLDV 250
            G SP  ILF +ELP A PT++ GLNQ I+M+L+MVV+A ++GA GLG +V  G+  +++
Sbjct: 190 SGASPKDILFKIELPTAAPTLLVGLNQCILMSLAMVVLAGLVGAGGLGAEVTRGLSRMEM 249

Query: 251 GKGLEAGIGIVILAVVLDRITQG 273
           G GL AG+ IV +A++LDR+++G
Sbjct: 250 GLGLRAGLAIVAIALLLDRLSRG 272


Lambda     K      H
   0.327    0.142    0.422 

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: 228
Number of extensions: 9
Number of successful extensions: 1
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: 285
Length of database: 283
Length adjustment: 26
Effective length of query: 259
Effective length of database: 257
Effective search space:    66563
Effective search space used:    66563
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: 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