GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Azospirillum brasilense Sp245

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate AZOBR_RS25595 AZOBR_RS25595 sugar ABC transporter ATP-binding protein

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



>FitnessBrowser__azobra:AZOBR_RS25595
          Length = 358

 Score =  369 bits (947), Expect = e-107
 Identities = 201/359 (55%), Positives = 246/359 (68%), Gaps = 4/359 (1%)

Query: 1   MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60
           M G+ L+ +RKS+G ++VIHG+DL++ +GEFV FVGPSGCGKSTLLR+IAGLEE +GGD+
Sbjct: 1   MAGVTLRGVRKSFGRIEVIHGVDLEVADGEFVAFVGPSGCGKSTLLRLIAGLEEPSGGDL 60

Query: 61  FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120
            I G+RVND PP+ RGIAMVFQSYALYPHMT YDNMAFG+ ++R  K  I  RVR AA +
Sbjct: 61  SIGGQRVNDRPPAARGIAMVFQSYALYPHMTAYDNMAFGLTLSRTDKGTIAERVRAAARL 120

Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180
           LQ+   LDR P+ LSGGQRQRVAIGRAI R P+VFLFDEPLSNLDA LRV  R+EIAKL 
Sbjct: 121 LQIEDLLDRKPRDLSGGQRQRVAIGRAIVREPQVFLFDEPLSNLDAGLRVQMRLEIAKLK 180

Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240
             +   TMIYVTHDQVEAMTLADRIVVL+AG +EQ G PLELY RP N FVA FIGSPAM
Sbjct: 181 ADLR-ATMIYVTHDQVEAMTLADRIVVLNAGRVEQAGTPLELYHRPRNRFVAGFIGSPAM 239

Query: 241 NVIPATITA-TGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFE 299
           N +       T     V L GG  + + V   A   G   + GVRPE + + +    L  
Sbjct: 240 NFLDVVSEGLTDGSVRVWLPGGVPLDIAVDGAAPAAGTPLTLGVRPEHVGLADGGAGLL- 298

Query: 300 GTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFDTNGQ 358
            T+  VE LG  T  +   L + + ++ ++ G   V  G+++R        HLF  +GQ
Sbjct: 299 ATILAVERLGGETHCH-AALEDGQRLLVRLDGDRPVAAGERLRLNLRGETAHLFGPDGQ 356


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: 422
Number of extensions: 24
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: 358
Length adjustment: 29
Effective length of query: 333
Effective length of database: 329
Effective search space:   109557
Effective search space used:   109557
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.

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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