GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AZOBR_RS08260 in Desulfovibrio vulgaris Hildenborough

Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate 209486 DVU0547 high-affinity branched chain amino acid ABC transporter, periplasmic branched chain amino acid-binding protein

Query= uniprot:G8ALJ3
         (366 letters)



>lcl|MicrobesOnline__882:209486 DVU0547 high-affinity branched chain
           amino acid ABC transporter, periplasmic branched chain
           amino acid-binding protein
          Length = 372

 Score =  208 bits (529), Expect = 2e-58
 Identities = 116/365 (31%), Positives = 182/365 (49%), Gaps = 4/365 (1%)

Query: 6   SLLVAVAATAMTASVAKAD-IAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLGQ 64
           +L+  +    M   V   D I +   G  +G  A++G       +      N  GG+ G+
Sbjct: 8   ALIAGMTVAVMAGPVFAGDTIKLGVPGAHSGDLASYGLPSANAAKIVAKMFNDKGGINGK 67

Query: 65  KLKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPAST 124
            +++   DD C P+ A   A +L   GV  V GH CSG++  A  +Y E   + +SP++T
Sbjct: 68  MVEVIPQDDQCKPEMATNAATKLVSDGVDIVLGHICSGATKAALPIYKEANKVVMSPSAT 127

Query: 125 NPKLTEQ-NLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQKA 183
            P LT+  +    FR    DDQQ ++   + ++    K +A+LHDK  YGKG A+  ++ 
Sbjct: 128 TPALTQSGDYPMFFRTISSDDQQAKLGVDFAIDKLGAKKIAVLHDKGDYGKGYAEYAKQF 187

Query: 184 LNAGGQKEKI-YEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNA 242
           +   G+   + +E  T G  DYSA+V K++ E  D V  GGYH EA  +  QM+ + +  
Sbjct: 188 IEQSGKATVVLFEGVTPGAVDYSAVVQKVRSEGADAVMFGGYHPEASKIVAQMRKKRMTT 247

Query: 243 PIVSGDALVTNEYWAITGPAGENTMMTFGPDPREMPEAKEAVEKFRKA-GYEPEGYTLYT 301
           P +S D +  + +  + G   E    +   D   +P  KEA+E  +K  G EP  +    
Sbjct: 248 PFISDDGVKDDTFIKVAGKDAEGVYASSSKDVSMLPMYKEAIELHKKEFGTEPGAFYKEA 307

Query: 302 YAALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWNNGQ 361
           +AA Q    A ++A ST++ K+ D LR N   T IGKI FD +GD     +  Y+  NG 
Sbjct: 308 FAAAQALLTAVQRAGSTETPKVVDALRNNFVETAIGKIKFDKRGDAEGTGFSMYQVKNGV 367

Query: 362 YAQVK 366
           Y ++K
Sbjct: 368 YVELK 372


Lambda     K      H
   0.312    0.129    0.366 

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: 340
Number of extensions: 18
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: 366
Length of database: 372
Length adjustment: 30
Effective length of query: 336
Effective length of database: 342
Effective search space:   114912
Effective search space used:   114912
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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