GapMind for catabolism of small carbon sources

 

Alignments 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)



>MicrobesOnline__882:209486
          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:

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