GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Paraburkholderia bryophila 376MFSha3.1

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate H281DRAFT_03228 H281DRAFT_03228 carbohydrate ABC transporter ATP-binding protein, CUT1 family

Query= uniprot:D8IPI1
         (406 letters)



>FitnessBrowser__Burk376:H281DRAFT_03228
          Length = 383

 Score =  335 bits (858), Expect = 2e-96
 Identities = 182/367 (49%), Positives = 241/367 (65%), Gaps = 13/367 (3%)

Query: 1   MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60
           MA I  + + K Y  G PV+  +DL IG+ EF V LGPSGCGKST+LRMIAGLED++ G 
Sbjct: 1   MASISLRGVQKAYGDGAPVIRDVDLEIGENEFCVFLGPSGCGKSTLLRMIAGLEDLTDGD 60

Query: 61  LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120
           L IGG V+ND+PA +R VAMVFQ+YAL+PHM+V++N+AFGL+  K P  EIDR+VRE A 
Sbjct: 61  LFIGGKVMNDVPAAQRGVAMVFQSYALFPHMTVFENMAFGLKLAKTPKDEIDRKVREAAR 120

Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180
           +L LEALLER+P+A+SGGQ+QR AI RAI++ P VFLFDEPLSNLDA LR Q R +I RL
Sbjct: 121 ILQLEALLERRPKALSGGQRQRVAIGRAIVRQPGVFLFDEPLSNLDATLRGQTRIEIARL 180

Query: 181 HQRL-RTTTVYVTHDQLEAMTLADRVILMQDGR-------IVQAGSPAELYRYPRNLFAA 232
           H++  + + VYVTHDQ+EAMTLAD+++L+  G+       I Q G+P ELY  PR+ F A
Sbjct: 181 HKQFAKASVVYVTHDQIEAMTLADKIVLLHAGKDTERYGSIAQIGAPLELYHRPRSRFVA 240

Query: 233 GFIGTPAMNFLSGTVQRQDGQ---LFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVR 289
           GFIG+P MNFL G +   D Q   + ++  H+   +  +  + L+ + AV L VRP+H+ 
Sbjct: 241 GFIGSPRMNFLPGRIASVDAQGVVVTLDHTHENVRVPADG-AALQVSQAVTLGVRPEHLE 299

Query: 290 IAGEREPAASLTCPVSVELVEILGADALL-TTRCGDQTLTALVPADRLPQPGATLTLALD 348
            A             +V LVE LG  + +   + G   L A  P D    PG    L + 
Sbjct: 300 FADLSSSHDDAVLSRTVSLVEQLGEHSYVHLDQPGGVALIAKAPGDTRLAPGDRANLRVP 359

Query: 349 QHELHVF 355
           +H  H+F
Sbjct: 360 RHATHLF 366


Lambda     K      H
   0.321    0.137    0.403 

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: 401
Number of extensions: 16
Number of successful extensions: 5
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: 406
Length of database: 383
Length adjustment: 31
Effective length of query: 375
Effective length of database: 352
Effective search space:   132000
Effective search space used:   132000
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: 50 (23.9 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