GapMind for catabolism of small carbon sources

 

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

Align Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate AO353_27980 AO353_27980 amino acid ABC transporter permease

Query= TCDB::Q9HU29
         (230 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_27980
          Length = 231

 Score =  206 bits (523), Expect = 4e-58
 Identities = 105/223 (47%), Positives = 148/223 (66%), Gaps = 1/223 (0%)

Query: 1   MSEWELILKWMPKMLQGAALTLELLAIAVVAGLALALPLGIARASRHWYVRAVPYAYIFF 60
           M ++ LI + +P    GA LTL++L I++  GL LA+PL + R SR   +    + Y + 
Sbjct: 1   MLDYNLIWENLPLYFSGALLTLKVLLISLAFGLMLAIPLALMRVSRSPLINFPAWLYTYA 60

Query: 61  FRGTPLLLQLFIVYYGLAQFEEVRKSAFWPYLRDPYWCALLTMTLHTAAYIAEILRGAIH 120
            RGTP+L+QLF++YYGLAQFE VR+S  WPYL    +CA L   ++T+AY AE+L G++ 
Sbjct: 61  IRGTPMLVQLFLIYYGLAQFEAVRQSVLWPYLSSATFCACLAFAINTSAYSAELLAGSLK 120

Query: 121 SVPVGEVEAARALGMSRRQALWHIILPRAVRIGLPAYSNEVILMLKASAVVYTVTLFDIM 180
           S P GE+EAA+A+GMSR      I+LP A+R  LP YSNEV++ML+ +++   VTL DI 
Sbjct: 121 STPNGEIEAAKAMGMSRLTLYRRILLPSALRRALPQYSNEVLMMLQTTSLASIVTLVDIT 180

Query: 181 GMARTIIARTYESMLFFCLAGALYLVITIVLTRIFRLIER-WL 222
           G ART+ +R Y     F  AG +YL +T +L R+F+L ER WL
Sbjct: 181 GAARTVSSRFYLPFEAFITAGLIYLALTFILVRLFKLAERHWL 223


Lambda     K      H
   0.332    0.142    0.443 

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: 167
Number of extensions: 4
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: 230
Length of database: 231
Length adjustment: 23
Effective length of query: 207
Effective length of database: 208
Effective search space:    43056
Effective search space used:    43056
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 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