GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Acidovorax sp. GW101-3H11

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 Ac3H11_552 Branched-chain amino acid ABC transporter, amino acid-binding protein (TC 3.A.1.4.1)

Query= TCDB::Q9L3M3
         (381 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_552
          Length = 384

 Score =  164 bits (416), Expect = 3e-45
 Identities = 120/364 (32%), Positives = 173/364 (47%), Gaps = 10/364 (2%)

Query: 4   SLLSAVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAG-GIN 62
           S L+AVAL A +A S      V IA AGP++G  A  G   + G   A  D+NA    I 
Sbjct: 15  SALTAVALAASVA-SAQDVQTVKIAHAGPVSGGIAHIGKDTENGVRLAIDDLNAQNLVIG 73

Query: 63  GEQIKIELG--DDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNH 120
           G++IK E+   DD  DP+Q  +VA K     V  V+GH  SG SIPAS +YA+  +    
Sbjct: 74  GKKIKFEIAAEDDAGDPRQATAVAQKLCDQKVAGVVGHLQSGTSIPASAIYAKCDLPHIT 133

Query: 121 PGRDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADET 180
                PDL   G   TFR    D+  GA    + ADH K   +A++ D+T YGQG+A   
Sbjct: 134 ASASNPDLTKPGHKTTFRLIANDNALGAALALFGADHQKLKSVAIIDDRTAYGQGVASVF 193

Query: 181 KKAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGL 240
           K      G+  V  E  N    DF A++  +K      I++GGL  +AG ++RQ    GL
Sbjct: 194 KATAQQKGLKVVAEEFTNDKATDFMAILTAIKNKKPDAIFYGGLDAQAGPMLRQMEQLGL 253

Query: 241 -KATLVSGDGIVSNELASIAGDAVA---GTLNTFGPDPTANPANKELVEKFKAAGFNP-E 295
                  GD + + +L  ++G   A    T  T G          +  +++ A      +
Sbjct: 254 GNVKYFGGDALCTEKLPELSGKTPALKNVTCATGGASVDKMQGGADWKKRYDAKFPGQFQ 313

Query: 296 AYTLYSYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIM 355
            Y+ Y+Y A   +A A K A S+DP+  A  +  K  +  V  +I+F  KG+   P   +
Sbjct: 314 IYSPYAYDAAMVLADAMKRANSVDPKVFAPFL-AKTEYKGVTANIAFTAKGELTTPAVTL 372

Query: 356 YEWK 359
           Y +K
Sbjct: 373 YTFK 376


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: 371
Number of extensions: 25
Number of successful extensions: 3
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: 384
Length adjustment: 30
Effective length of query: 351
Effective length of database: 354
Effective search space:   124254
Effective search space used:   124254
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 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