GapMind for catabolism of small carbon sources

 

Alignments 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_RS07345 BWI76_RS07345 family 3 extracellular solute-binding protein

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



>FitnessBrowser__Koxy:BWI76_RS07345
          Length = 258

 Score =  217 bits (552), Expect = 2e-61
 Identities = 111/256 (43%), Positives = 154/256 (60%), Gaps = 2/256 (0%)

Query: 1   MKKLVLLGALALSVLSLPTFADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEE 60
           MKK +LL  +AL   +     + K ++ G++  + PF  K P G + GFD D+GNA+C +
Sbjct: 1   MKKSLLLW-VALMASTSALAVENKEIRFGVDPTFAPFEWKDPQGKLAGFDIDLGNAICAQ 59

Query: 61  MKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITEDRKKSVDFTNKYYNTPARLVMKAGT 120
           ++ KCVWVE  FDG+IPALK RK DAILS M +TE RK+ + F++K YN P  LV +  T
Sbjct: 60  LQAKCVWVESNFDGIIPALKARKFDAILSGMYMTEKRKEQIGFSDKLYNGPVFLVARKNT 119

Query: 121 AVSENLAELKGKNIGVQRGSIHERFAREVLAPLGAEIKPYGSQNEIYLDVAAGRLDGTVA 180
                + +LKGK IGV++GS  E +  +     G  I  Y   + +  D+ +GR+DG V 
Sbjct: 120 LAGNTVEQLKGKTIGVEQGSAQETYVNQHWRTAGINIVAYQGADRVVQDLESGRIDGAVL 179

Query: 181 DATLLDDGFLKTDAGKGFAFVGPAFTDVKYFGDGVGIAVRK-GDALKDKINTAIAAIREN 239
              + D  FL+   GK FAFVG    D K FG G  I +RK  DAL+ +IN AIA I  +
Sbjct: 180 SGMMADYSFLQQPQGKDFAFVGGHLKDDKLFGAGAAIGLRKEDDALRQEINGAIARILAD 239

Query: 240 GKYKQIQDKYFAFDIY 255
           G YK++  KYF+FD+Y
Sbjct: 240 GTYKKLAGKYFSFDVY 255


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: 212
Number of extensions: 8
Number of successful extensions: 3
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: 258
Length adjustment: 24
Effective length of query: 233
Effective length of database: 234
Effective search space:    54522
Effective search space used:    54522
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 (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