GapMind for catabolism of small carbon sources

 

Aligments for a candidate for argT in Paraburkholderia bryophila 376MFSha3.1

Align lysine/arginine/ornithine ABC transporter, periplasmic lysine/arginine/ornithine-binding protein ArgT (characterized)
to candidate H281DRAFT_00224 H281DRAFT_00224 amino acid ABC transporter substrate-binding protein, PAAT family

Query= CharProtDB::CH_003045
         (260 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_00224 H281DRAFT_00224 amino
           acid ABC transporter substrate-binding protein, PAAT
           family
          Length = 258

 Score =  306 bits (783), Expect = 4e-88
 Identities = 147/259 (56%), Positives = 191/259 (73%), Gaps = 5/259 (1%)

Query: 1   MKKTVLALSLLI-GLGATAASYAALPQTVRIGTDTTYAPFSSKDAKGEFIGFDIDLGNEM 59
           MKK  L ++L +   GA A  +    +TVRIG D +Y PF SK A G+ +GFD+DL   +
Sbjct: 1   MKKLALCVALAVMATGAMAKEW----KTVRIGVDASYPPFESKAASGQVVGFDVDLTKAL 56

Query: 60  CKRMQVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAA 119
           C RM VKC WV  DFD +IP+LK KK DAI+SSL++TDKR+++I FSDKL+ A +R+IA 
Sbjct: 57  CARMNVKCVWVEQDFDGIIPALKGKKFDAIVSSLTVTDKRREQIDFSDKLFDAPARMIAK 116

Query: 120 KGSPIQPTLESLKGKHVGVLQGSTQEAYANDNWRTKGVDVVAYANQDLIYSDLTAGRLDA 179
            GSP+ PT ESLKGK +GV QG+TQEAYA   W  KGV VV Y NQD +Y+DLT+GRLDA
Sbjct: 117 AGSPLLPTAESLKGKRIGVEQGTTQEAYAKAYWEPKGVTVVPYQNQDQVYADLTSGRLDA 176

Query: 180 ALQDEVAASEGFLKQPAGKEYAFAGPSVKDKKYFGDGTGVGLRKDDTELKAAFDKALTEL 239
           ALQDE+ A  GFLK P GK +A+AGP VKD K  G+GT +GLRK+D +L+  F++AL ++
Sbjct: 177 ALQDEIQADAGFLKTPRGKGFAWAGPEVKDPKTIGEGTAIGLRKEDADLRTMFNRALAQV 236

Query: 240 RQDGTYDKMAKKYFDFNVY 258
            QDGT+ K+ K+YFDF++Y
Sbjct: 237 HQDGTFTKLEKQYFDFDIY 255


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: 262
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: 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 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