GapMind for catabolism of small carbon sources

 

Alignments for a candidate for argT in Pseudomonas fluorescens FW300-N2E3

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 AO353_29015 AO353_29015 ABC transporter substrate-binding protein

Query= TCDB::P09551
         (260 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_29015
          Length = 262

 Score =  260 bits (665), Expect = 2e-74
 Identities = 127/263 (48%), Positives = 178/263 (67%), Gaps = 7/263 (2%)

Query: 1   MKKSILALSLLV----GLSTAASSYAALPETVRIGTDTTYAPFSSKDAKGDFVGFDIDLG 56
           M K I A+SL+     GL+ AA       + +R+G D TY P   K+  G   GF +D+ 
Sbjct: 1   MNKMIAAVSLVFLTASGLAGAADWSG---KVLRLGIDPTYPPLEYKNQDGTLTGFGVDIA 57

Query: 57  NEMCKRMQVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRL 116
           + +C  +  KC WV S +D +IP L A+K DAI SS+++T KRQ++IAFSDK+  A +RL
Sbjct: 58  DALCAELHAKCVWVESSWDGMIPGLLARKFDAIASSMTVTPKRQEQIAFSDKVSNAPARL 117

Query: 117 IAAKGSPIQPTLDSLKGKHVGVLQGSTQEAYANETWRSKGVDVVAYANQDLVYSDLAAGR 176
           +  +GS +QPT++SLKGK +GV QGSTQEA+A   W  +GV++++Y NQD VY+DL  GR
Sbjct: 118 VIKRGSDLQPTVESLKGKRIGVEQGSTQEAFAKAVWGKQGVEILSYQNQDQVYADLVVGR 177

Query: 177 LDAALQDEVAASEGFLKQPAGKDFAFAGSSVKDKKYFGDGTGVGLRKDDAELTAAFNKAL 236
           LDA+LQ  + AS GFL +P GKD+ FAG ++ + ++FG G G+G+RK D EL    NKAL
Sbjct: 178 LDASLQGSIQASYGFLNKPVGKDYEFAGGTLDNPEFFGVGDGIGVRKSDVELREDLNKAL 237

Query: 237 GELRQDGTYDKMAKKYFDFNVYG 259
             +  +GTY K+ KKYFDF++YG
Sbjct: 238 ATILANGTYAKINKKYFDFDIYG 260


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: 247
Number of extensions: 12
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: 262
Length adjustment: 25
Effective length of query: 235
Effective length of database: 237
Effective search space:    55695
Effective search space used:    55695
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