GapMind for catabolism of small carbon sources

 

Alignments for a candidate for argT in Klebsiella michiganensis M5al

Align lysine/arginine/ornithine ABC transporter, periplasmic lysine/arginine/ornithine-binding protein ArgT (characterized)
to candidate BWI76_RS19240 BWI76_RS19240 ABC transporter substrate-binding protein

Query= CharProtDB::CH_003045
         (260 letters)



>FitnessBrowser__Koxy:BWI76_RS19240
          Length = 257

 Score =  234 bits (597), Expect = 1e-66
 Identities = 116/255 (45%), Positives = 167/255 (65%), Gaps = 2/255 (0%)

Query: 6   LALSLLIGLGATAASYAALP-QTVRIGTDTTYAPFSSKDAKGEFIGFDIDLGNEMCKRMQ 64
           + L+ L+   A +A  AA    T+  G D  Y PF      GE  GFDID+ N +C +++
Sbjct: 3   IRLAALLACMALSAPLAAQQFDTISFGVDGGYPPFDVLAPSGEITGFDIDIANALCTQLK 62

Query: 65  VKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSPI 124
            KC +V   F+++I +L A K DAII+SL+ITD+R++E+ F+D+ Y + ++L+A KGSP+
Sbjct: 63  AKCVFVKQPFESMIAALNAHKFDAIIASLNITDERKKEVDFTDRYYRSAAQLVARKGSPL 122

Query: 125 QPTLESLKGKHVGVLQGSTQEAYANDNWRTKGVDVVAYANQDLIYSDLTAGRLDAALQDE 184
            P   SLKGK VGV  GST EA+A  NW   GV +V YANQD +Y DL +GR+DAALQD 
Sbjct: 123 LPDAASLKGKTVGVQTGSTHEAFAKANWANHGVKIVGYANQDNVYLDLLSGRIDAALQDN 182

Query: 185 VAASEGFLKQPAGKEYAFAGPSVKDKKYFGDGTGVGLRKDDTELKAAFDKALTELRQDGT 244
           + A+ GF+  P G+++AFAGP ++D     D  G+ + KD+  L+ A + A+  +R DGT
Sbjct: 183 IQAATGFIDTPRGQKFAFAGPVIQDGGISSD-VGIAVNKDNPALRDALNGAIKAIRADGT 241

Query: 245 YDKMAKKYFDFNVYG 259
           YD + KKYF F++YG
Sbjct: 242 YDAIQKKYFSFDIYG 256


Lambda     K      H
   0.315    0.132    0.374 

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: 232
Number of extensions: 12
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: 260
Length of database: 257
Length adjustment: 24
Effective length of query: 236
Effective length of database: 233
Effective search space:    54988
Effective search space used:    54988
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: 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