GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AO353_03055 in Klebsiella michiganensis M5al

Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate BWI76_RS20340 BWI76_RS20340 histidine ABC transporter substrate-binding protein HisJ

Query= reanno::pseudo1_N1B4:Pf1N1B4_3431
         (257 letters)



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

 Score =  229 bits (584), Expect = 4e-65
 Identities = 116/260 (44%), Positives = 166/260 (63%), Gaps = 3/260 (1%)

Query: 1   MKKLVLLGALALSVLSLPTFADEKP--LKIGIEAAYPPFASKAPDGSIVGFDYDIGNALC 58
           MKK VL  +L + + S  +     P  ++IG +A Y PF+SK   G  VGFD D+GN LC
Sbjct: 1   MKKTVLALSLMMGICSASSAFAALPQSIRIGTDATYAPFSSKDAKGDFVGFDIDLGNELC 60

Query: 59  EEMKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITEDRKKSVDFTNKYYNTPARLVMKA 118
             +KVKC WV  +FD LIP+LK +KIDAI+SS+SITE R++ + F++K Y   +RL+   
Sbjct: 61  SRIKVKCTWVGSDFDSLIPSLKAKKIDAIISSLSITEKRQQEIAFSDKLYAADSRLIAAK 120

Query: 119 GTAVSENLAELKGKNIGVQRGSIHERFAREVLAPLGAEIKPYGSQNEIYLDVAAGRLDGT 178
           G+ +   L  LKGK++GV +GS  E +  E     G ++  Y +Q+ IY D++AGRLD  
Sbjct: 121 GSPIQPTLESLKGKHVGVLQGSTQEAYGNERWRSHGVDVVAYQNQDLIYSDLSAGRLDAA 180

Query: 179 VADATLLDDGFLKTDAGKGFAFVGPAFTDVKYFGDGVGIAVRKGDA-LKDKINTAIAAIR 237
           + D     +GFLK  AGK FAF GP+  D K+FGDG GI +RK D+ LK   + A+A +R
Sbjct: 181 LQDEVAASEGFLKQPAGKDFAFAGPSVKDKKFFGDGTGIGLRKDDSELKAAFDKALADMR 240

Query: 238 ENGKYKQIQDKYFAFDIYGK 257
           ++G Y ++  KYF F++YG+
Sbjct: 241 KDGTYDKMAKKYFDFNVYGE 260


Lambda     K      H
   0.318    0.138    0.394 

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: 218
Number of extensions: 10
Number of successful extensions: 2
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: 257
Length of database: 260
Length adjustment: 24
Effective length of query: 233
Effective length of database: 236
Effective search space:    54988
Effective search space used:    54988
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 (21.7 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, the preprint on GapMind for carbon sources, 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