GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate H281DRAFT_03228 H281DRAFT_03228 carbohydrate ABC transporter ATP-binding protein, CUT1 family

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



>FitnessBrowser__Burk376:H281DRAFT_03228
          Length = 383

 Score =  358 bits (918), Expect = e-103
 Identities = 195/371 (52%), Positives = 254/371 (68%), Gaps = 15/371 (4%)

Query: 1   MTGLLLKDIRKSYG-AVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGD 59
           M  + L+ ++K+YG    VI  +DL+I E EF VF+GPSGCGKSTLLRMIAGLE++T GD
Sbjct: 1   MASISLRGVQKAYGDGAPVIRDVDLEIGENEFCVFLGPSGCGKSTLLRMIAGLEDLTDGD 60

Query: 60  MFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAAD 119
           +FI G+ +NDVP ++RG+AMVFQSYAL+PHMTV++NMAFG+++A+  K+EIDR+VR AA 
Sbjct: 61  LFIGGKVMNDVPAAQRGVAMVFQSYALFPHMTVFENMAFGLKLAKTPKDEIDRKVREAAR 120

Query: 120 MLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKL 179
           +LQL   L+R PKALSGGQRQRVAIGRAI R P VFLFDEPLSNLDA LR  TRIEIA+L
Sbjct: 121 ILQLEALLERRPKALSGGQRQRVAIGRAIVRQPGVFLFDEPLSNLDATLRGQTRIEIARL 180

Query: 180 SERMSDTTMIYVTHDQVEAMTLADRIVVLSA-------GHIEQVGAPLELYERPANLFVA 232
            ++ +  +++YVTHDQ+EAMTLAD+IV+L A       G I Q+GAPLELY RP + FVA
Sbjct: 181 HKQFAKASVVYVTHDQIEAMTLADKIVLLHAGKDTERYGSIAQIGAPLELYHRPRSRFVA 240

Query: 233 RFIGSPAMNVIPATITATGQQTAVSLAGGKSVTLDVPTN--ASENGKTASFGVRPEDLRV 290
            FIGSP MN +P  I +   Q  V         + VP +  A +  +  + GVRPE L  
Sbjct: 241 GFIGSPRMNFLPGRIASVDAQGVVVTLDHTHENVRVPADGAALQVSQAVTLGVRPEHLEF 300

Query: 291 TEA----DDFLFEGTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTAD 346
            +     DD +   TVS+VE LGE + ++++       +IAK PG  R+  GD+      
Sbjct: 301 ADLSSSHDDAVLSRTVSLVEQLGEHSYVHLD-QPGGVALIAKAPGDTRLAPGDRANLRVP 359

Query: 347 KAKLHLFDTNG 357
           +   HLF  +G
Sbjct: 360 RHATHLFTEDG 370


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: 405
Number of extensions: 17
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: 383
Length adjustment: 30
Effective length of query: 332
Effective length of database: 353
Effective search space:   117196
Effective search space used:   117196
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.

Links

Downloads

Related tools

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