GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artJ in Klebsiella michiganensis M5al

Align Putative ABC transporter arginine-binding protein 2 (characterized)
to candidate BWI76_RS09515 BWI76_RS09515 arginine ABC transporter substrate-binding protein

Query= SwissProt::P30859
         (243 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS09515 BWI76_RS09515 arginine ABC
           transporter substrate-binding protein
          Length = 243

 Score =  453 bits (1165), Expect = e-132
 Identities = 222/243 (91%), Positives = 233/243 (95%)

Query: 1   MKKVLIAALIAGFSLSATAAETIRFATEASYPPFESIDANNQIVGFDVDLAQALCKEIDA 60
           MKKVLIAAL+AG SLSATAA+TIRFATEASYPPFESIDANN+IVGFDVDLA ALCKEIDA
Sbjct: 1   MKKVLIAALLAGMSLSATAAQTIRFATEASYPPFESIDANNKIVGFDVDLANALCKEIDA 60

Query: 61  TCTFSNQAFDSLIPSLKFRRVEAVMAGMDITPEREKQVLFTTPYYDNSALFVGQQGKYTS 120
           TCTF+NQAFDSLIPSLKFRR +AVMAGMDITPEREKQVLFTTPYY+NSALFVGQQGK+TS
Sbjct: 61  TCTFTNQAFDSLIPSLKFRRFDAVMAGMDITPEREKQVLFTTPYYENSALFVGQQGKFTS 120

Query: 121 VDQLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDGVFGDTAVVTE 180
           +D LKGKKVGVQNGTTHQKFI DKHPEITTVPYDSYQNAKLDLQNGRID VFGDTAVVTE
Sbjct: 121 IDALKGKKVGVQNGTTHQKFITDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVTE 180

Query: 181 WLKDNPKLAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKLNTALEKVKKDGTYETIYNKW 240
           WLK NPKLAAVGDKVTDKDYFGTGLGIA+RQGNTELQQK N ALEKVK DGTY++IYNKW
Sbjct: 181 WLKSNPKLAAVGDKVTDKDYFGTGLGIALRQGNTELQQKFNAALEKVKSDGTYQSIYNKW 240

Query: 241 FQK 243
           FQK
Sbjct: 241 FQK 243


Lambda     K      H
   0.316    0.133    0.380 

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: 336
Number of extensions: 9
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: 243
Length of database: 243
Length adjustment: 23
Effective length of query: 220
Effective length of database: 220
Effective search space:    48400
Effective search space used:    48400
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