GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artM in Pseudomonas stutzeri RCH2

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 GFF136 Psest_0136 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= TCDB::Q9HU29
         (230 letters)



>lcl|FitnessBrowser__psRCH2:GFF136 Psest_0136 amine acid ABC
           transporter, permease protein, 3-TM region,
           His/Glu/Gln/Arg/opine family
          Length = 229

 Score =  330 bits (845), Expect = 2e-95
 Identities = 158/227 (69%), Positives = 191/227 (84%)

Query: 4   WELILKWMPKMLQGAALTLELLAIAVVAGLALALPLGIARASRHWYVRAVPYAYIFFFRG 63
           WE+ +KW+P  + GA LTL+L+ ++V+AGL +A+PLGIAR+SRH  VRA+PY YIFFFRG
Sbjct: 3   WEIFIKWLPSFIDGAWLTLQLVGVSVIAGLIVAVPLGIARSSRHLAVRALPYGYIFFFRG 62

Query: 64  TPLLLQLFIVYYGLAQFEEVRKSAFWPYLRDPYWCALLTMTLHTAAYIAEILRGAIHSVP 123
           TPLL+QLF+VYYG+AQF+ VR+SA WPYLRDPYWCA++TMTLHTAAYIAEI+RGAI +VP
Sbjct: 63  TPLLVQLFLVYYGMAQFDVVRQSALWPYLRDPYWCAIITMTLHTAAYIAEIIRGAIQNVP 122

Query: 124 VGEVEAARALGMSRRQALWHIILPRAVRIGLPAYSNEVILMLKASAVVYTVTLFDIMGMA 183
            GE+EAARALGMSR QAL HIILPRA RIGLPAYSNEVILMLKASA+  T+TL ++ GMA
Sbjct: 123 HGEIEAARALGMSRSQALLHIILPRATRIGLPAYSNEVILMLKASALASTITLLELTGMA 182

Query: 184 RTIIARTYESMLFFCLAGALYLVITIVLTRIFRLIERWLRVDATQGR 230
           R I ARTY     F  AG +YL+I  +L + F+L+ERWLRVDA QGR
Sbjct: 183 RKIAARTYLHEEMFLTAGLIYLLIAFILMQGFKLLERWLRVDACQGR 229


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: 231
Number of extensions: 6
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: 229
Length adjustment: 23
Effective length of query: 207
Effective length of database: 206
Effective search space:    42642
Effective search space used:    42642
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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