GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artJ in Klebsiella michiganensis M5al

Align lysine/arginine/ornithine ABC transporter, periplasmic lysine/arginine/ornithine-binding protein ArgT (characterized)
to candidate BWI76_RS20340 BWI76_RS20340 histidine ABC transporter substrate-binding protein HisJ

Query= CharProtDB::CH_003045
         (260 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS20340 BWI76_RS20340 histidine ABC
           transporter substrate-binding protein HisJ
          Length = 260

 Score =  457 bits (1176), Expect = e-133
 Identities = 221/260 (85%), Positives = 250/260 (96%)

Query: 1   MKKTVLALSLLIGLGATAASYAALPQTVRIGTDTTYAPFSSKDAKGEFIGFDIDLGNEMC 60
           MKKTVLALSL++G+ + ++++AALPQ++RIGTD TYAPFSSKDAKG+F+GFDIDLGNE+C
Sbjct: 1   MKKTVLALSLMMGICSASSAFAALPQSIRIGTDATYAPFSSKDAKGDFVGFDIDLGNELC 60

Query: 61  KRMQVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAK 120
            R++VKCTWV SDFD+LIPSLKAKKIDAIISSLSIT+KRQQEIAFSDKLYAADSRLIAAK
Sbjct: 61  SRIKVKCTWVGSDFDSLIPSLKAKKIDAIISSLSITEKRQQEIAFSDKLYAADSRLIAAK 120

Query: 121 GSPIQPTLESLKGKHVGVLQGSTQEAYANDNWRTKGVDVVAYANQDLIYSDLTAGRLDAA 180
           GSPIQPTLESLKGKHVGVLQGSTQEAY N+ WR+ GVDVVAY NQDLIYSDL+AGRLDAA
Sbjct: 121 GSPIQPTLESLKGKHVGVLQGSTQEAYGNERWRSHGVDVVAYQNQDLIYSDLSAGRLDAA 180

Query: 181 LQDEVAASEGFLKQPAGKEYAFAGPSVKDKKYFGDGTGVGLRKDDTELKAAFDKALTELR 240
           LQDEVAASEGFLKQPAGK++AFAGPSVKDKK+FGDGTG+GLRKDD+ELKAAFDKAL ++R
Sbjct: 181 LQDEVAASEGFLKQPAGKDFAFAGPSVKDKKFFGDGTGIGLRKDDSELKAAFDKALADMR 240

Query: 241 QDGTYDKMAKKYFDFNVYGD 260
           +DGTYDKMAKKYFDFNVYG+
Sbjct: 241 KDGTYDKMAKKYFDFNVYGE 260


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: 357
Number of extensions: 10
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: 260
Length adjustment: 24
Effective length of query: 236
Effective length of database: 236
Effective search space:    55696
Effective search space used:    55696
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