GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17595 in Pseudomonas stutzeri RCH2

Align ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale)
to candidate GFF136 Psest_0136 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= uniprot:A0A1N7UBU2
         (233 letters)



>FitnessBrowser__psRCH2:GFF136
          Length = 229

 Score =  103 bits (256), Expect = 4e-27
 Identities = 67/211 (31%), Positives = 106/211 (50%), Gaps = 2/211 (0%)

Query: 12  PMLAQGAWMTLKLAFLALALSLALGLIAAAAKLSSAKWLRVPATLYTTLIRSVPDLVLIL 71
           P    GAW+TL+L  +++   L + +    A+ S    +R     Y    R  P LV + 
Sbjct: 11  PSFIDGAWLTLQLVGVSVIAGLIVAVPLGIARSSRHLAVRALPYGYIFFFRGTPLLVQLF 70

Query: 72  LIFYSLQLWLNDLSEVFGWDYFEIDPFTAGVITLGFIYGAYFTENFRGAILSVPVGQLEA 131
           L++Y +  + + + +   W Y   DP+   +IT+     AY  E  RGAI +VP G++EA
Sbjct: 71  LVYYGMAQF-DVVRQSALWPYLR-DPYWCAIITMTLHTAAYIAEIIRGAIQNVPHGEIEA 128

Query: 132 ATAYGLSRWQRFHLVLFPQLMRFALPGLGNNWLVLLKSTALVSIIGLSDLVKAAQNAGKT 191
           A A G+SR Q    ++ P+  R  LP   N  +++LK++AL S I L +L   A+     
Sbjct: 129 ARALGMSRSQALLHIILPRATRIGLPAYSNEVILMLKASALASTITLLELTGMARKIAAR 188

Query: 192 TNEPLYFLILAGLMYLVITTLSNRVLKRLER 222
           T       + AGL+YL+I  +  +  K LER
Sbjct: 189 TYLHEEMFLTAGLIYLLIAFILMQGFKLLER 219


Lambda     K      H
   0.327    0.141    0.428 

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: 155
Number of extensions: 1
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: 233
Length of database: 229
Length adjustment: 23
Effective length of query: 210
Effective length of database: 206
Effective search space:    43260
Effective search space used:    43260
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: 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:

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