GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ in Azospirillum thiophilum BV-S

Align BraC, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC (characterized)
to candidate WP_144428388.1 AL072_RS26400 ABC transporter substrate-binding protein

Query= TCDB::Q9L3M3
         (381 letters)



>NCBI__GCF_001305595.1:WP_144428388.1
          Length = 367

 Score =  345 bits (885), Expect = 1e-99
 Identities = 172/359 (47%), Positives = 234/359 (65%), Gaps = 4/359 (1%)

Query: 5   LLSAVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGINGE 64
           +LS  A    L     A AD+ +AV GP+TG  A +G QL++GAE+A ADINA GGI G 
Sbjct: 2   MLSCAAAMLHLTTQSAAAADITVAVVGPMTGQYATYGDQLRRGAEKAVADINAKGGILGS 61

Query: 65  QIKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPGRD 124
           ++++ +GDD  DPKQ ++VAN+  A GV  + GH+ S  SIPAS VYA+ G L+  P   
Sbjct: 62  KLQLIVGDDACDPKQAVAVANQMVARGVALINGHYCSSSSIPASAVYADAGTLQISPAST 121

Query: 125 EP---DLHGTGLW-NTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADET 180
            P   D      W N FR  GRDD QGA A +Y+A+HFK  ++AV+HDKT YG+GLADE 
Sbjct: 122 NPRFTDEAAAKKWINIFRISGRDDDQGATAARYIAEHFKGKRLAVIHDKTAYGKGLADEM 181

Query: 181 KKAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGL 240
           KKA NA G+ EV+Y+ IN G+KDF+ LI+ +K+  + ++Y+GG H EAGLI+RQA +Q  
Sbjct: 182 KKAANALGIQEVLYDSINQGEKDFTPLISLLKQNAIDVVYFGGYHAEAGLIVRQAREQAF 241

Query: 241 KATLVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPEAYTLY 300
               + GD +++ E  +I+G A  GTL TF PDP  NP  K LV +F+A G +P  YTLY
Sbjct: 242 ATRFIGGDTLMTEEFYTISGPAGDGTLMTFHPDPRKNPVAKPLVGQFQAQGIDPTGYTLY 301

Query: 301 SYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEWK 359
           SY+ +Q  A AAK AGS+D   ++  +K    F T +G +SF++KGD   P ++ YEWK
Sbjct: 302 SYSVLQVFAEAAKTAGSVDMAKLSAVLKSGKSFDTAVGTLSFNQKGDVSRPDFVFYEWK 360


Lambda     K      H
   0.314    0.132    0.383 

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: 402
Number of extensions: 16
Number of successful extensions: 2
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: 381
Length of database: 367
Length adjustment: 30
Effective length of query: 351
Effective length of database: 337
Effective search space:   118287
Effective search space used:   118287
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 (22.0 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