GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Dethiosulfovibrio salsuginis USBA 82

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_085545256.1 B9Y55_RS10130 ABC transporter ATP-binding protein

Query= uniprot:G8ALJ0
         (294 letters)



>NCBI__GCF_900177735.1:WP_085545256.1
          Length = 503

 Score = 89.0 bits (219), Expect = 2e-22
 Identities = 72/239 (30%), Positives = 112/239 (46%), Gaps = 29/239 (12%)

Query: 17  LTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTLRHADGK 76
           +T  F G+ A + +  +   GE+ A++G NGAGK+TL N ++G Y P  G + +    G 
Sbjct: 4   ITKSFQGIKANDQIDLTLKKGEVLALLGENGAGKSTLMNVLSGIYLPDGGTIDI----GG 59

Query: 77  EFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIAGLLGLP 136
             L  R P   IS  A +    Q+  L    +V EN+++               GL  LP
Sbjct: 60  TRLSFRSPNDAIS--AGIGMVHQHFMLVPSQTVWENMVL---------------GLPDLP 102

Query: 137 SYTRTER---EAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVMLCLD 193
                 +   E   ++K +   V   E   W+   L  G Q+R+EI + +     +L LD
Sbjct: 103 QILPKGKIISEITAISKQYGLEVDP-EAIIWQ---LSIGEQQRVEILKTLYRNAQVLILD 158

Query: 194 EPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISDGD 252
           EP A L P+E+  L + +  + +E + G++ I H +  VM ISD V VL  G+ I   D
Sbjct: 159 EPTAVLTPQEARSLFNTIKRMTEEGR-GIIFISHKLDEVMEISDRVTVLRKGKLIGTVD 216



 Score = 42.0 bits (97), Expect = 3e-08
 Identities = 53/225 (23%), Positives = 93/225 (41%), Gaps = 16/225 (7%)

Query: 23  GLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTLRHADGKEFLLER 82
           GL A++ VS     G+I  + G  G G+T L   + G    T G+L L+   GKE + + 
Sbjct: 262 GLKALDQVSLELREGQILGLAGVAGNGQTELCQVMAGLRKMTSGKLILK---GKE-VTDS 317

Query: 83  MPGYRISQKAS-VARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIAGLLGLPSYTRT 141
            P   I      +    +   +   M V EN  + ++ +   A G  I        +   
Sbjct: 318 SPRELIDGGIRYIPADRKGTGMVSNMDVRENSTLKRYWRRPVARGVLI-------DWKAV 370

Query: 142 EREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVMLCLDEPAAGLNP 201
            + A+ + K +      +E       NL  G  ++L + R +   P +L    P  GL+ 
Sbjct: 371 LKHALGIVKNFNVDTPSVE---TPVRNLSGGNIQKLMLGRELSDIPKVLIAMNPTWGLDV 427

Query: 202 RESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGR 246
             +  + + L   R E    + LI  D+  +M++SD + V+  G+
Sbjct: 428 AATRFVREQLLEER-EKGAAIFLISEDLDELMSLSDRIAVMYRGK 471


Lambda     K      H
   0.319    0.137    0.397 

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: 305
Number of extensions: 18
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 294
Length of database: 503
Length adjustment: 30
Effective length of query: 264
Effective length of database: 473
Effective search space:   124872
Effective search space used:   124872
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 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