GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00895 in Burkholderia phytofirmans PsJN

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate BPHYT_RS19450 BPHYT_RS19450 metal-dependent hydrolase

Query= uniprot:D8J1T6
         (255 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS19450 BPHYT_RS19450
           metal-dependent hydrolase
          Length = 594

 Score =  223 bits (567), Expect = 9e-63
 Identities = 117/250 (46%), Positives = 167/250 (66%), Gaps = 2/250 (0%)

Query: 3   QTLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTF 62
           + LL +    K+FGGL A+N V   ++ GQI GLIGPNGAGK+T FN++TG+ Q  +G  
Sbjct: 344 EDLLTVNKARKQFGGLVAVNDVSFEVKAGQIIGLIGPNGAGKSTTFNLVTGVLQATSGEI 403

Query: 63  ELDGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKA 122
              G+     +  E+ K GI RTFQ+++L   MTVLENV +G H+R +  V+ +V R  +
Sbjct: 404 TFCGERIDSLSSREIVKRGIGRTFQHVKLLPGMTVLENVAIGAHLRGQAGVWRSVVRLNS 463

Query: 123 AREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAA 182
           A  EEA +  ++ + +  VG+ Q     A  L+ G QR LEIARAL  DP LL LDEPAA
Sbjct: 464 A--EEARLMAEAARQIRRVGLEQHMYDEAGSLALGQQRILEIARALCCDPTLLLLDEPAA 521

Query: 183 GMNATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQK 242
           G+   EKL L +LL +++AEG ++LL+EHD+  +M L +R+ V+++G  IAEG+P +VQ+
Sbjct: 522 GLRYQEKLQLADLLRRLKAEGMSVLLVEHDMDFVMNLTDRLVVMEFGTRIAEGLPQEVQQ 581

Query: 243 NPAVIEAYLG 252
           +PAV+EAYLG
Sbjct: 582 DPAVLEAYLG 591


Lambda     K      H
   0.320    0.138    0.394 

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: 369
Number of extensions: 14
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: 255
Length of database: 594
Length adjustment: 30
Effective length of query: 225
Effective length of database: 564
Effective search space:   126900
Effective search space used:   126900
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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