GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Shewanella amazonensis SB2B

Align Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized)
to candidate 6937240 Sama_1410 phosphate ABC transporter, ATP-binding protein (RefSeq)

Query= SwissProt::P0AAF6
         (242 letters)



>FitnessBrowser__SB2B:6937240
          Length = 272

 Score =  138 bits (348), Expect = 1e-37
 Identities = 95/250 (38%), Positives = 142/250 (56%), Gaps = 16/250 (6%)

Query: 2   SIQLNGINCFYGAHQALFDITLDCPQGETLVLLGPSGAGKSSLLRVLNLLEMPRSGTLNI 61
           ++++  +N  YG  QALFD+++  P+      +GPSG GKS+LLR +N +        NI
Sbjct: 25  ALEIQNLNLHYGTKQALFDVSMKIPKKRVTAFIGPSGCGKSTLLRCINRMN-DLVDNCNI 83

Query: 62  AGNHFDFTKTPSDKAI--RDLRRNVGMVFQQYNLWPHLTVQQNLIEAPCRVLGLSKDQAL 119
            G      +   DKA+    LRRNVGMVFQ+ N +P  ++ +N++    R+ G++  + L
Sbjct: 84  TGEIRLHEQNIYDKAVDVAALRRNVGMVFQRPNPFPK-SIYENVVYG-LRLQGINNRREL 141

Query: 120 ARA-EKLLERLRL-KPYSDRYPLH-----LSGGQQQRVAIARALMMEPQVLLFDEPTAAL 172
             A E+ L    +     DR  LH     LSGGQQQR+ IARA+ +EP+VLL DEPT+AL
Sbjct: 142 DEACERSLRGAAIWDEVKDR--LHDNAFGLSGGQQQRLVIARAIAIEPEVLLLDEPTSAL 199

Query: 173 DPEITAQIVSIIRELAETNITQVIVTHEVEVARKTASRVVYMENGHIVEQGDA-SCFTEP 231
           DP  T  I  +I EL +   T VIVTH ++ A + + +  +M  G +VE  D  + FT P
Sbjct: 200 DPISTLTIEELITEL-KAKYTVVIVTHNMQQAARVSDQTAFMYMGELVEYADTNTIFTTP 258

Query: 232 QTEAFKNYLS 241
                ++Y++
Sbjct: 259 SQRKTEDYIT 268


Lambda     K      H
   0.320    0.135    0.391 

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: 134
Number of extensions: 11
Number of successful extensions: 4
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: 242
Length of database: 272
Length adjustment: 24
Effective length of query: 218
Effective length of database: 248
Effective search space:    54064
Effective search space used:    54064
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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 (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