GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisQ in Klebsiella michiganensis M5al

Align Histidine transport system permease protein HisQ (characterized)
to candidate BWI76_RS19235 BWI76_RS19235 polar amino acid ABC transporter inner membrane subunit

Query= SwissProt::P0A2I9
         (228 letters)



>FitnessBrowser__Koxy:BWI76_RS19235
          Length = 230

 Score =  194 bits (492), Expect = 2e-54
 Identities = 92/221 (41%), Positives = 153/221 (69%)

Query: 1   MLYGFSGVILQGAIVTLELALSSVVLAVLIGLVGAGAKLSQNRVTGLIFEGYTTLIRGVP 60
           M+  +  ++L+GA ++L + LSS+++A+L+GL+ +  KL       L    YTTL+RG+P
Sbjct: 1   MVADYLPLLLRGAALSLCVMLSSLLVALLLGLINSLIKLFGPPWLRLFSTAYTTLVRGIP 60

Query: 61  DLVLMLLIFYGLQIALNVVTDSLGIDQIDIDPMVAGIITLGFIYGAYFTETFRGAFMAVP 120
           +LV+MLL+F+G ++ +N++   +G+  +  +  ++G++ +GF++GAY+TETFRGAF+ V 
Sbjct: 61  ELVIMLLLFFGGEMLVNLLLGLVGLGPVRFNTFISGVLAIGFVFGAYYTETFRGAFLTVD 120

Query: 121 KGHIEAATAFGFTHGQTFRRIMFPAMMRYALPGIGNNWQVILKATALVSLLGLEDVVKAT 180
            G  EAA A+G      FRR+M P M+ +A+PGI NNW  ++KA+ALVS+LGLED+V   
Sbjct: 121 SGQTEAAQAYGMRPWTVFRRVMLPQMLSFAIPGINNNWLGLMKASALVSILGLEDMVWLA 180

Query: 181 QLAGKSTWEPFYFAVVCGLIYLVFTTVSNGVLLLLERRYSV 221
           + AG++T +PF F  +  LIY+V T +S+ +   L +RY++
Sbjct: 181 EQAGRATQKPFLFYFLVSLIYMVITALSSWLFSRLAKRYAL 221


Lambda     K      H
   0.328    0.144    0.422 

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: 186
Number of extensions: 8
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: 228
Length of database: 230
Length adjustment: 23
Effective length of query: 205
Effective length of database: 207
Effective search space:    42435
Effective search space used:    42435
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 46 (22.3 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