GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtB' in Azospirillum brasilense Sp245

Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate AZOBR_RS15675 AZOBR_RS15675 ABC transporter permease

Query= uniprot:Q31RP0
         (377 letters)



>FitnessBrowser__azobra:AZOBR_RS15675
          Length = 224

 Score = 87.0 bits (214), Expect = 4e-22
 Identities = 65/195 (33%), Positives = 99/195 (50%), Gaps = 10/195 (5%)

Query: 179 WLVVILAIA-----LVLFVSWLAQRQRSPRDWRWLYGA-IAVVTVLMLLTQLSWPQQLQP 232
           WL V L+I      L++ +     +   P+  RW+  A I VV     L Q+     +  
Sbjct: 22  WLTVQLSIGAMVLGLIVAILCALGKTSGPKPVRWVINAYIEVVRNTPFLVQIFL---IFF 78

Query: 233 GQIRGGLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQ 292
           G    G+RLS +  AL+  +V   GA+ TEIIR GI S+  GQ EA  ALGL   Q    
Sbjct: 79  GLPTMGVRLSPDLAALI-AMVVNVGAYATEIIRAGIESIQKGQIEAGLALGLKPLQVFRY 137

Query: 293 IVVPQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLT 352
           IV+  ALR + P+L SQ++    +SS+  A+   +L + A    +QT R  E+++++   
Sbjct: 138 IVIKPALRTVYPALTSQFILLMLSSSVVSAISADELTSVANNIQSQTFRSFEIYIVVTGI 197

Query: 353 YLAINAVISAGMNGL 367
           YL +  + SA   G+
Sbjct: 198 YLMLAMMFSALFAGI 212



 Score = 31.6 bits (70), Expect = 2e-05
 Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 1/52 (1%)

Query: 93  IAIG-LILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQLIVWYF 143
           ++IG ++L  ++  L  +   S    +R +   Y+ VVRNTP L+Q+ + +F
Sbjct: 27  LSIGAMVLGLIVAILCALGKTSGPKPVRWVINAYIEVVRNTPFLVQIFLIFF 78


Lambda     K      H
   0.326    0.140    0.445 

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: 188
Number of extensions: 11
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: 377
Length of database: 224
Length adjustment: 26
Effective length of query: 351
Effective length of database: 198
Effective search space:    69498
Effective search space used:    69498
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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