GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatM in Escherichia coli BW25113

Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate 16032 b1918 predicted transporter subunit: membrane component of ABC superfamily (NCBI)

Query= SwissProt::P0AER5
         (224 letters)



>FitnessBrowser__Keio:16032
          Length = 222

 Score =  139 bits (350), Expect = 4e-38
 Identities = 80/214 (37%), Positives = 122/214 (57%), Gaps = 8/214 (3%)

Query: 9   IVPSLPYLLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYVNVFRSIPL 68
           ++ SLP+LL G   TL++++  +  G+L G +LA+MRLS   PV W A+ Y+++FR  PL
Sbjct: 8   VIDSLPFLLKGAGYTLQLSIGGMFFGLLLGFILALMRLSPIWPVRWLARFYISIFRGTPL 67

Query: 69  VMVLLWFYLIVPGFLQNVLGLSPKNDIRLISAMVAFSMFEAAYYSEIIRAGIQSISRGQS 128
           +  L   Y  +P F    + L P     + SAM+  S+  AAY +E +RA I SI +GQ 
Sbjct: 68  IAQLFMIYYGLPQF---GIELDP-----IPSAMIGLSLNTAAYAAETLRAAISSIDKGQW 119

Query: 129 SAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVLSLADFFRTASTIG 188
            AA ++GMT WQ+M+  ILPQA R  +P L    I L +DTSL   + + + FR A  I 
Sbjct: 120 EAAASIGMTPWQTMRRAILPQAARVALPPLSNSFISLVKDTSLAATIQVPELFRQAQLIT 179

Query: 189 ERDGTQVEMILFAGFVYFVISLSASLLVSYLKRR 222
            R      M L A  +Y++++   S L ++ + +
Sbjct: 180 SRTLEVFTMYLAASLIYWIMATVLSTLQNHFENQ 213


Lambda     K      H
   0.330    0.140    0.412 

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: 126
Number of extensions: 8
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: 224
Length of database: 222
Length adjustment: 22
Effective length of query: 202
Effective length of database: 200
Effective search space:    40400
Effective search space used:    40400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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