GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Azospirillum brasilense Sp245

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate AZOBR_RS27980 AZOBR_RS27980 sugar ABC transporter ATP-binding protein

Query= uniprot:D8IPI1
         (406 letters)



>FitnessBrowser__azobra:AZOBR_RS27980
          Length = 360

 Score =  319 bits (818), Expect = 7e-92
 Identities = 173/363 (47%), Positives = 226/363 (62%), Gaps = 9/363 (2%)

Query: 1   MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60
           MA +  + L K Y GG PVLH + + I DGEFV L+GPSGCGKST+LRMIAGLE+   G 
Sbjct: 1   MASVIIRDLRKSY-GGTPVLHGVSVDIADGEFVALVGPSGCGKSTLLRMIAGLEEAGEGE 59

Query: 61  LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120
           +RIGG +VND+P ++R++AMVFQNYALYPHM+V  N+ F L        EI  RV   A 
Sbjct: 60  IRIGGRLVNDVPPKDRDIAMVFQNYALYPHMTVAQNLGFALTLKDVDRGEIAARVARAAE 119

Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180
           +L L ALL+R+P  +SGGQ+QR A+ RAI++ P +FLFDEPLSNLDAKLR Q+R +IK L
Sbjct: 120 VLGLSALLDRRPGQLSGGQRQRVAMGRAIVRDPRLFLFDEPLSNLDAKLRVQMRAEIKAL 179

Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240
           HQRLRT+ +YVTHDQ+EAMT+ADR+++M+DGR+ QAG+P +LY  P N F AGFIG+PAM
Sbjct: 180 HQRLRTSAIYVTHDQIEAMTMADRIVVMRDGRVEQAGAPLDLYDRPANRFVAGFIGSPAM 239

Query: 241 NFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASL 300
           NFL+G +       F         L+              L +RP+H  I  E       
Sbjct: 240 NFLTGRIAVNGRASFRLDGGPDLPLSAVPLE--ADGRPAVLGLRPEHALIDPEE------ 291

Query: 301 TCPVSVELVEILGADALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFDVESG 360
             P+ V +VE  G++  +  +   Q    +       +PG  L L L     H+FD   G
Sbjct: 292 GVPLHVAVVEPTGSETQVVGQLAGQPFVGVFRERVAARPGDILPLRLPAASAHLFDAGEG 351

Query: 361 ENL 363
             L
Sbjct: 352 RRL 354


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: 445
Number of extensions: 20
Number of successful extensions: 2
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: 360
Length adjustment: 30
Effective length of query: 376
Effective length of database: 330
Effective search space:   124080
Effective search space used:   124080
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.

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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