GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artP in Marinobacter adhaerens HP15

Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate GFF2243 HP15_2193 amino-acid ABC transporter ATP-binding protein-like protein

Query= SwissProt::P54537
         (240 letters)



>lcl|FitnessBrowser__Marino:GFF2243 HP15_2193 amino-acid ABC
           transporter ATP-binding protein-like protein
          Length = 256

 Score =  262 bits (670), Expect = 4e-75
 Identities = 132/240 (55%), Positives = 173/240 (72%)

Query: 1   MIKVEKLSKSFGKHEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTITI 60
           +I+VE + K +G   VLK+++ T+ +GE + + GPSGSGKSTF+RC+N LE+   G I +
Sbjct: 15  IIRVEGMHKWYGDFHVLKDLNLTVDQGERIVICGPSGSGKSTFIRCINRLEEHQQGKIIV 74

Query: 61  KDTEITKPKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQAAQEKAEDL 120
              E+T    +   VR  +GMVFQHF+LFPH TVLEN   +P+ V+K  ++ A+  A + 
Sbjct: 75  DGIELTDDVRHIDTVRREVGMVFQHFNLFPHLTVLENCCLSPIWVRKTPRKEAEASAMEY 134

Query: 121 LRKVGLFEKRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVKEVLQVMK 180
           L +V + ++ N +P +LSGGQ+QRVAIARAL M P IMLFDEPTSALDPEM+KEVL VM 
Sbjct: 135 LERVKIPDQANKFPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMIKEVLDVMI 194

Query: 181 ELVETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSKRAQDFLEKIL 240
           EL  +GMTM+ VTHEMGFAK VADRV+FMD G IVE   P EFF +P+  R Q FL++IL
Sbjct: 195 ELAGSGMTMLCVTHEMGFAKTVADRVIFMDGGEIVEQAPPHEFFTNPQEARTQKFLQQIL 254


Lambda     K      H
   0.317    0.134    0.368 

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: 212
Number of extensions: 8
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: 240
Length of database: 256
Length adjustment: 24
Effective length of query: 216
Effective length of database: 232
Effective search space:    50112
Effective search space used:    50112
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 (21.6 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 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