GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16925 in Pseudomonas fluorescens FW300-N2E3

Align Arabinose ABC transporter permease (characterized, see rationale)
to candidate AO353_21390 AO353_21390 ABC transporter

Query= uniprot:A0A161GM94
         (322 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_21390
          Length = 340

 Score =  177 bits (449), Expect = 3e-49
 Identities = 96/280 (34%), Positives = 161/280 (57%), Gaps = 17/280 (6%)

Query: 55  LAISTTGIAACTMLYCLASGHFDLSVGSVIACAGVVAAVVMRDTN------------SVF 102
           L +S  G+ A  +   + +   DLS GSV+A + ++AA + + ++             V+
Sbjct: 61  LQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVW 120

Query: 103 LGISAALVMGLIVGLINGIVIAKLRVNALITTLATMQIVRGLAYIFANGKAVGVSQESFF 162
           + + A L +GL+ G ING +IA   +   I TL  M   RGLA  +  G+ V +  +S+ 
Sbjct: 121 IPVIAGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYT 180

Query: 163 VFGNGQMFGVPVPILITIVCFLFFGWLLNYTTYGRNTMAIGGNQEAALLAGVNVDRTKII 222
             G+G M     P++I +V  + F   L YT YG+ T AIGGN +AA  +G+NV R  +I
Sbjct: 181 AIGHGAM-----PVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVI 235

Query: 223 IFAVHGVIGALAGVILASRMTSGQPMIGQGFELTVISACVLGGVSLSGGIGMIRHVIAGV 282
           ++++ G++  LAGV+ ++R  +GQ  +G  +EL  I+A V+GG SL+GG+G I   + G 
Sbjct: 236 VYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGA 295

Query: 283 LILAIIENAMNLKNIDTFYQYVIRGSILLLAVVIDRLKQR 322
           LIL ++ +      +D + Q +I+G I+++AVVID+ + +
Sbjct: 296 LILGVMASGFTFVGVDAYIQDIIKGLIIVIAVVIDQYRNK 335


Lambda     K      H
   0.330    0.144    0.420 

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: 304
Number of extensions: 20
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: 322
Length of database: 340
Length adjustment: 28
Effective length of query: 294
Effective length of database: 312
Effective search space:    91728
Effective search space used:    91728
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 (21.8 bits)
S2: 49 (23.5 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