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 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)

Query= SwissProt::P0AAF6
         (242 letters)



>FitnessBrowser__SB2B:6936480
          Length = 341

 Score =  140 bits (353), Expect = 3e-38
 Identities = 86/241 (35%), Positives = 132/241 (54%), Gaps = 9/241 (3%)

Query: 2   SIQLNGINCFYGAHQALFDITLDCPQGETLVLLGPSGAGKSSLLRVLNLLEMPRSGTLNI 61
           ++ + G++  Y   Q L  + L   QGE   LLGPSG GK++LLR +  L+   +G++ I
Sbjct: 3   TLSIQGLHSDYRGEQVLRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISAGSIAI 62

Query: 62  AGNHFDFTKTPSDKAIRDLRRNVGMVFQQYNLWPHLTVQQNLIEAPCRVLGLSKDQALAR 121
            G     T +     +   +R++GM+FQ Y L+PHLTV  N++     V  L K     R
Sbjct: 63  NGK----TVSADGCFVAPEKRSIGMIFQDYALFPHLTVADNILFG---VRQLDKQSRSVR 115

Query: 122 AEKLLERLRLKPYSDRYPLHLSGGQQQRVAIARALMMEPQVLLFDEPTAALDPEITAQIV 181
            E++L  ++L+    RYP  LSGGQQQRV+IARAL  EP +LL DEP + +D ++   ++
Sbjct: 116 LEEMLSLVKLEGLGKRYPHELSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALM 175

Query: 182 SIIRELAET-NITQVIVTHEVEVARKTASRVVYMENGHIVEQG-DASCFTEPQTEAFKNY 239
             IR + +  N++ V VTH  + A   A  +   E G IV+ G   + +  P T    ++
Sbjct: 176 LEIRAILKARNVSAVFVTHSKDEAFAFADTLALFEAGRIVQHGIPETLYQSPNTPYVADF 235

Query: 240 L 240
           L
Sbjct: 236 L 236


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: 177
Number of extensions: 7
Number of successful extensions: 3
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: 341
Length adjustment: 26
Effective length of query: 216
Effective length of database: 315
Effective search space:    68040
Effective search space used:    68040
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