GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Herbaspirillum seropedicae SmR1

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 HSERO_RS17350 HSERO_RS17350 ABC transporter substrate-binding protein

Query= TCDB::Q9L3M3
         (381 letters)



>FitnessBrowser__HerbieS:HSERO_RS17350
          Length = 380

 Score =  206 bits (524), Expect = 9e-58
 Identities = 131/367 (35%), Positives = 187/367 (50%), Gaps = 11/367 (2%)

Query: 3   KSLLSAVALTAMLAFSGNAWADVLIAVA--GPLTGPNAAFGAQLQKGAEQAAADINAAG- 59
           KS +  +     LAF+G A++  ++ +A  GPL+GPNA  G   + GA  A  ++NA G 
Sbjct: 4   KSAIIPLTAAIGLAFAGAAYSQEVVKIAHVGPLSGPNAHMGKDNENGARMAVDELNAKGF 63

Query: 60  GINGEQIKIEL--GDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGIL 117
            I G+++K EL   DD SDPKQ  +VA K     V  VIGH NSG +IPAS++Y++ GI 
Sbjct: 64  TIGGKKVKFELVGEDDASDPKQATAVATKLVDQKVAAVIGHLNSGTTIPASKIYSDAGIP 123

Query: 118 RNHPGRDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLA 177
           +  P    P     G    FR    D Q GA  GKY        +IAV+ D+T YGQG+A
Sbjct: 124 QVSPSATNPKYTQQGFKTAFRVVANDAQLGAALGKYAVQKLGTKQIAVIDDRTAYGQGVA 183

Query: 178 DETKKAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAAD 237
           DE  K   AAG T V  +  N    DF+A++  +K     ++++GG+    G ++RQ   
Sbjct: 184 DEFAKGAKAAGGTIVGTQYTNDKATDFNAILTSLKGKKPDVVFFGGMDAVGGPMLRQMKQ 243

Query: 238 QGLKATLVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAA-----GF 292
            G+ A  + GDGI +  L  +AGD +             + A K+ ++ F+AA     G 
Sbjct: 244 LGISAKFMGGDGICTGSLPGLAGDGLGDDQVICAEAGGVDEAGKKGMDDFRAAYKKKFGI 303

Query: 293 NPEAYTLYSYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPG 352
           +      Y+Y A  T+A A   AGS DP+     +  K     V G I+FD KGD K   
Sbjct: 304 DVVYNAAYAYDATMTVADAMAKAGSADPKKYLPEL-AKISHKGVTGVIAFDAKGDIKDGS 362

Query: 353 YIMYEWK 359
             +Y +K
Sbjct: 363 LTLYTYK 369


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: 435
Number of extensions: 24
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: 381
Length of database: 380
Length adjustment: 30
Effective length of query: 351
Effective length of database: 350
Effective search space:   122850
Effective search space used:   122850
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.

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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