GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Brucella inopinata BO1

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_008509836.1 BIBO1_RS16200 ABC transporter ATP-binding protein

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



>NCBI__GCF_000182725.1:WP_008509836.1
          Length = 333

 Score =  370 bits (950), Expect = e-107
 Identities = 201/359 (55%), Positives = 252/359 (70%), Gaps = 27/359 (7%)

Query: 1   MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60
           M  L L+D+RKS+G+ +VI G+D+DI+ GEF+VFVGPSGCGKSTLLR+IAGLEEIT G +
Sbjct: 1   MAELQLRDVRKSFGSFEVIKGVDMDIRPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTL 60

Query: 61  FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120
            I+G  VN+  PS+RGIAMVFQSYALYPHMTVY+NMAFGM++A +S++E   R+  AA+M
Sbjct: 61  SINGAVVNNFNPSRRGIAMVFQSYALYPHMTVYENMAFGMQLASKSRQECKARIHAAAEM 120

Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180
           LQLTPYL+RLP+ LSGGQRQRVAIGRAI R+PKVFLFDEPLSNLDAALRVATR+EIA+L 
Sbjct: 121 LQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIARLH 180

Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240
           + M DTTMIYVTHDQVEAMTLADRI VL  G +EQ+G PLELYE+P +LFVA FIGSP M
Sbjct: 181 QSMEDTTMIYVTHDQVEAMTLADRICVLRDGRVEQIGTPLELYEKPNSLFVAGFIGSPKM 240

Query: 241 NVIPATITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFEG 300
           N +      TG                     +E     + G+R E L +       + G
Sbjct: 241 NFL------TGPH-------------------AEPFGAHTVGLRSEHLAIVPERGH-WSG 274

Query: 301 TVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFDTNGQS 359
            V   E LG  T +YI+ L   EP++ +  G++    G+ +  +     +H FD  G++
Sbjct: 275 QVVHTEILGSDTYVYID-LGLEEPLVVRESGVSARKPGEALSISPTGDHVHRFDEKGRA 332


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: 367
Number of extensions: 12
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 362
Length of database: 333
Length adjustment: 29
Effective length of query: 333
Effective length of database: 304
Effective search space:   101232
Effective search space used:   101232
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 24 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