GapMind for catabolism of small carbon sources

 

Alignments for a candidate for argT in Klebsiella michiganensis M5al

Align ArgT aka B2310, component of Histidine/Arginine/Lysine (basic amino acid) uptake porter, HisJ/ArgT/HisP/HisM/HisQ [R, R, C, M, M, respectively] (Gilson et al. 1982). HisJ binds L-His (preferred), but 1-methyl-L-His and 3-methyl-L-His also bind, while the dipeptide carnosine binds weakly; D-histidine and the histidine degradation products, histamine, urocanic acid and imidazole do not bind. L-Arg, homo-L-Arg, and post-translationally modified methylated Arg-analogs also bind with the exception of symmetric dimethylated-L-Arg. L-Lys and L-Orn show weaker interactions with HisJ and methylated and acetylated Lys variants show poor binding.The carboxylate groups of these amino acids and their variants are essential (characterized)
to candidate BWI76_RS07345 BWI76_RS07345 family 3 extracellular solute-binding protein

Query= TCDB::P09551
         (260 letters)



>FitnessBrowser__Koxy:BWI76_RS07345
          Length = 258

 Score =  255 bits (651), Expect = 7e-73
 Identities = 126/258 (48%), Positives = 169/258 (65%), Gaps = 3/258 (1%)

Query: 1   MKKSILALSLLVGLSTAASSYAALPETVRIGTDTTYAPFSSKDAKGDFVGFDIDLGNEMC 60
           MKKS+L   L V L  + S+ A   + +R G D T+APF  KD +G   GFDIDLGN +C
Sbjct: 1   MKKSLL---LWVALMASTSALAVENKEIRFGVDPTFAPFEWKDPQGKLAGFDIDLGNAIC 57

Query: 61  KRMQVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAK 120
            ++Q KC WV S+FD +IP+LKA+K DAI+S + +T+KR+++I FSDKLY     L+A K
Sbjct: 58  AQLQAKCVWVESNFDGIIPALKARKFDAILSGMYMTEKRKEQIGFSDKLYNGPVFLVARK 117

Query: 121 GSPIQPTLDSLKGKHVGVLQGSTQEAYANETWRSKGVDVVAYANQDLVYSDLAAGRLDAA 180
            +    T++ LKGK +GV QGS QE Y N+ WR+ G+++VAY   D V  DL +GR+D A
Sbjct: 118 NTLAGNTVEQLKGKTIGVEQGSAQETYVNQHWRTAGINIVAYQGADRVVQDLESGRIDGA 177

Query: 181 LQDEVAASEGFLKQPAGKDFAFAGSSVKDKKYFGDGTGVGLRKDDAELTAAFNKALGELR 240
           +   + A   FL+QP GKDFAF G  +KD K FG G  +GLRK+D  L    N A+  + 
Sbjct: 178 VLSGMMADYSFLQQPQGKDFAFVGGHLKDDKLFGAGAAIGLRKEDDALRQEINGAIARIL 237

Query: 241 QDGTYDKMAKKYFDFNVY 258
            DGTY K+A KYF F+VY
Sbjct: 238 ADGTYKKLAGKYFSFDVY 255


Lambda     K      H
   0.315    0.132    0.369 

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: 209
Number of extensions: 4
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: 260
Length of database: 258
Length adjustment: 24
Effective length of query: 236
Effective length of database: 234
Effective search space:    55224
Effective search space used:    55224
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