GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Bacteroides thetaiotaomicron VPI-5482

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate 353284 BT3758 acetylornithine aminotransferase (NCBI ptt file)

Query= BRENDA::Q0K2K2
         (423 letters)



>FitnessBrowser__Btheta:353284
          Length = 373

 Score =  199 bits (506), Expect = 1e-55
 Identities = 137/394 (34%), Positives = 212/394 (53%), Gaps = 38/394 (9%)

Query: 30  RAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFTHTAYQIVPYQGYVT 89
           + +   +WD  G  Y D   G AV++ GH HP  ++ I+ Q+      +  ++  +    
Sbjct: 16  KGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATLGFYSNSVIN-KLQQQ 74

Query: 90  LAERINALVPIQGLNKTALF--TTGAEAVENAIKIARAHTGRPGVIAFSGAFHGRTLLGM 147
           +AER+     I G    +LF   +GAEA ENA+K+A  + GR  VI+FS AFHGRT L +
Sbjct: 75  VAERLGK---ISGYEDYSLFLINSGAEANENALKLASFYNGRTKVISFSKAFHGRTSLAV 131

Query: 148 ALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQALEGLFKTDIDPARVAAIIVE 207
             T             P+ I  AP  +  +G  T   L  +E + K ++    V A+I+E
Sbjct: 132 EATNN-----------PTII--APINN--NGHVTYLPLNDIEAM-KQELAKGDVCAVIIE 175

Query: 208 PVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMSHHDVEPDLITM 267
            +QG GG +    +FM+ LR VC + G +LI DE+Q+G+GR+GK FA  ++ ++PD+IT+
Sbjct: 176 GIQGVGGIKIPTTEFMQELRKVCTETGTILILDEIQSGYGRSGKFFAHQYNHIQPDIITV 235

Query: 268 AKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVAAAHAVIDVIEEEKLCERSAS 327
           AK +  G P++ V    + M  P+ G LG T+ GN LA +AA AV+DVIE++ L E + +
Sbjct: 236 AKGIGNGFPMAGV--LISPMFKPVYGQLGTTFGGNHLACSAALAVMDVIEQDNLVENAKA 293

Query: 328 LGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCDPATGQPSAEHAKRVQTRALEAGLVL 387
           +G    ++LL + K  P + EVRG G M+  EF +P          K +++R +    V 
Sbjct: 294 VG----DYLLEELKKFPQIKEVRGRGLMIGLEFEEP---------IKELRSRLIYDEHV- 339

Query: 388 LTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQAL 421
            T  +  NV+R L PL +   + D  LA   + L
Sbjct: 340 FTGASGTNVLRLLPPLCLSMEEADEFLARFKRVL 373


Lambda     K      H
   0.321    0.136    0.400 

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: 355
Number of extensions: 16
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: 423
Length of database: 373
Length adjustment: 31
Effective length of query: 392
Effective length of database: 342
Effective search space:   134064
Effective search space used:   134064
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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