GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Desulfacinum infernum DSM 9756

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein

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



>NCBI__GCF_900129305.1:WP_073037934.1
          Length = 365

 Score =  284 bits (726), Expect = 3e-81
 Identities = 159/353 (45%), Positives = 217/353 (61%), Gaps = 15/353 (4%)

Query: 6   LKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDGE 65
           ++D+RK YG V  + G+   ++EG+ +V +GPSGCGK+TLLR+IAGLE +T G + I G 
Sbjct: 5   IRDVRKDYGRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIHIAGT 64

Query: 66  RVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQLTP 125
            V  +PP KR I+MVFQSYAL+PH+ V +N+ FG+++ +   +EI+RR++   D+L L+ 
Sbjct: 65  DVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVDLLGLSG 124

Query: 126 YLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERMSD 185
            LD  P  LSGG +QRVA+GRAI     V L DEPLSNLDA LR + R EI  L  R+  
Sbjct: 125 RLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQRRLG- 183

Query: 186 TTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVIPA 245
            TMIYVTHDQVEAMT+ADRIV++  G I Q  +P   YERPAN FVARFIG+P MN++P 
Sbjct: 184 ITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNIVPL 243

Query: 246 TITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFEGTVSIV 305
             T  G   A    GG+ +   +  +         FG+RPE+LR+ E+        V+  
Sbjct: 244 CPTQGG---AALEPGGRLLFPGMDPD------RYLFGIRPENLRLAESGQ---PAMVTGR 291

Query: 306 EALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFDTNGQ 358
           E LG  T +  E  +  + +I +  G   +  G  V  T D   ++LFD   Q
Sbjct: 292 EYLGSDTFVSCE--IHGQEVIVRTRGRRNIREGTVVHLTWDPGDVNLFDARTQ 342


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: 361
Number of extensions: 15
Number of successful extensions: 3
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: 365
Length adjustment: 29
Effective length of query: 333
Effective length of database: 336
Effective search space:   111888
Effective search space used:   111888
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 Apr 09 2024. 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