GapMind for catabolism of small carbon sources

 

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

Align Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter periplasmic binding 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_11995 AO353_11995 amino acid ABC transporter

Query= TCDB::Q9HU31
         (250 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_11995
          Length = 251

 Score =  412 bits (1058), Expect = e-120
 Identities = 200/251 (79%), Positives = 225/251 (89%), Gaps = 1/251 (0%)

Query: 1   MKNYKKILLAAAATLAFALDASAADKLRIGTEGAYPPFNGIDASGQAVGFDLDIGKALCA 60
           M+ YKK+LLAAAATL F+ +A AA+KL++G E AYPPFN  DASGQ VGFD DIG ALCA
Sbjct: 1   MQTYKKLLLAAAATLVFSANAMAAEKLKMGIEAAYPPFNNKDASGQVVGFDKDIGDALCA 60

Query: 61  KMKTECEVVTSDWDGIIPALNAKKFDFIVASMSITDERKQAVDFTDPYYTNKLQFVAPKS 120
           KM+ ECEVVTSDWDGIIPALNAKKFDF+V+S+SIT+ERKQAVDFTDPYY+NKLQF+APK+
Sbjct: 61  KMRVECEVVTSDWDGIIPALNAKKFDFLVSSLSITEERKQAVDFTDPYYSNKLQFIAPKN 120

Query: 121 VDFKTDKDSLKGKVIGAQRATIAGTWLEDNMADVVTIKLYDTQENAYLDLSSGRLDGVLA 180
           VD KTDKDSLKGK+IG QRAT+AGTWLEDN  + VTIKLYDTQENAYLDL+SGR+D +LA
Sbjct: 121 VDLKTDKDSLKGKIIGTQRATLAGTWLEDNYGNDVTIKLYDTQENAYLDLTSGRVDAILA 180

Query: 181 DKFVQYDWLKSDAGKEFEFKGEPVFDNDKIGIAVRKG-DPLREKLNAALKEIVADGTYKK 239
           DK+  YDWLKSDAGK +EFKGEPV  +DKIGIAVRKG D LR KLNAALKEIV+DGTYKK
Sbjct: 181 DKYANYDWLKSDAGKNYEFKGEPVVASDKIGIAVRKGQDELRNKLNAALKEIVSDGTYKK 240

Query: 240 INDKYFPFSIY 250
           INDKYFPFSIY
Sbjct: 241 INDKYFPFSIY 251


Lambda     K      H
   0.317    0.135    0.392 

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: 324
Number of extensions: 13
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: 250
Length of database: 251
Length adjustment: 24
Effective length of query: 226
Effective length of database: 227
Effective search space:    51302
Effective search space used:    51302
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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