GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artP in Marinobacter adhaerens HP15

Align AotP aka PA0892, component of Arginine/ornithine (but not lysine) porter (characterized)
to candidate GFF3087 HP15_3030 histidine/lysine/arginine/ornithine transporter subunit

Query= TCDB::O30506
         (254 letters)



>lcl|FitnessBrowser__Marino:GFF3087 HP15_3030
           histidine/lysine/arginine/ornithine transporter subunit
          Length = 256

 Score =  333 bits (855), Expect = 2e-96
 Identities = 162/244 (66%), Positives = 205/244 (84%)

Query: 7   QDLHKRYGSHEVLKGVSLAAKAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLNGEE 66
           +D++K +   EVLKG+SL  + GDV+S+IGSSGSGKSTFLRCINLLE P +G I+++G+ 
Sbjct: 10  RDIYKTFDQLEVLKGISLETRKGDVVSLIGSSGSGKSTFLRCINLLETPTSGDIIVHGDP 69

Query: 67  LKLVPGRDGALKAADSRQLQRMRSRLSMVFQHFNLWSHMSALENVIEAPVHVLGVSKKEA 126
           ++    R G    AD++Q++ +R++LSMVFQ FNLWSHM+ LEN+IEAPVHVL V KKEA
Sbjct: 70  IRFTTNRKGERIPADNKQVELIRAKLSMVFQSFNLWSHMTVLENIIEAPVHVLKVPKKEA 129

Query: 127 IEKAEHYLAKVGVAHRKDAYPAHMSGGEQQRVAIARALAVEPEVMLFDEPTSALDPELVG 186
           IE+AE YL KVG+  RKD YPA MSGG+QQR AIARALA+EPEVMLFDEPTSALDPELVG
Sbjct: 130 IERAEAYLNKVGIYERKDYYPAQMSGGQQQRAAIARALAMEPEVMLFDEPTSALDPELVG 189

Query: 187 EVLKVMQDLAQEGRTMVVVTHEMGFAREVSNQLVFLHKGLVEEHGCPKEVLANPQSDRLK 246
           EVLKVMQ LA+EGRTM+VVTHEM FAR+VS+Q++FLH+G++EE G P++V  +P S+R+K
Sbjct: 190 EVLKVMQGLAEEGRTMIVVTHEMAFARDVSSQVLFLHQGVIEEQGTPEKVFDHPDSERMK 249

Query: 247 QFLS 250
           QFL+
Sbjct: 250 QFLT 253


Lambda     K      H
   0.317    0.133    0.373 

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: 217
Number of extensions: 3
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: 254
Length of database: 256
Length adjustment: 24
Effective length of query: 230
Effective length of database: 232
Effective search space:    53360
Effective search space used:    53360
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: 47 (22.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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