GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Herbaspirillum seropedicae SmR1

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate HSERO_RS22750 HSERO_RS22750 sugar ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc03065
         (362 letters)



>FitnessBrowser__HerbieS:HSERO_RS22750
          Length = 377

 Score =  363 bits (931), Expect = e-105
 Identities = 193/363 (53%), Positives = 246/363 (67%), Gaps = 4/363 (1%)

Query: 1   MTGLLLKDIRKSY-GAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGD 59
           M  + +K +RK+Y G  DV+ G++LDI++GEF V VGPSGCGKSTLLRM+ GLEEI+GG+
Sbjct: 1   MAHVNIKQLRKTYDGRADVLAGLNLDIRDGEFCVLVGPSGCGKSTLLRMLCGLEEISGGE 60

Query: 60  MFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAAD 119
           + I G+ VN +PP++RGIAMVFQSYALYPHM VY NMAFG+++A  SK +ID R+R AA 
Sbjct: 61  LAIGGQVVNHLPPAERGIAMVFQSYALYPHMNVYKNMAFGLKVAGNSKSDIDARIRHAAA 120

Query: 120 MLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKL 179
           +L++   L RLP+ LSGGQRQRVAIGRAI R P++FLFDEPLSNLDAALRV TR+EIAKL
Sbjct: 121 ILKIDHLLQRLPRELSGGQRQRVAIGRAIVRQPRLFLFDEPLSNLDAALRVQTRLEIAKL 180

Query: 180 SERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPA 239
             +++  T++YVTHDQVEAMTL D+IVV+  G I+Q G PLELY++P NLFVA FIGSP 
Sbjct: 181 HRQLA-ATIVYVTHDQVEAMTLGDKIVVMHEGRIQQAGTPLELYQQPQNLFVAGFIGSPK 239

Query: 240 MNVIPATITATGQQ-TAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLF 298
           MN     +T        V +AGG  +  DV       G   + G+R E +R    D    
Sbjct: 240 MNFFQGVVTRCDDSGVQVEIAGGLRLLADVDPLGVTPGAAVTLGLRAEQIREGLGDGQPL 299

Query: 299 EGTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFDTNGQ 358
            G V++VE LGE   LY+  L     I+ +  G   V  G  +  +      HLFD  GQ
Sbjct: 300 HGVVNLVEHLGEANFLYVT-LDGGHDIVVRGDGNRNVDIGQPIALSVHSHAFHLFDAQGQ 358

Query: 359 SYR 361
           + R
Sbjct: 359 ALR 361


Lambda     K      H
   0.320    0.137    0.387 

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: 392
Number of extensions: 12
Number of successful extensions: 4
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: 362
Length of database: 377
Length adjustment: 30
Effective length of query: 332
Effective length of database: 347
Effective search space:   115204
Effective search space used:   115204
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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