GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Cupriavidus basilensis 4G11

Align Gamma aminobutyrate transaminase 1, mitochondrial; Gamma-aminobutyrate transaminase isozyme 1; LeGABA-TP1; SlGABA-T1; EC 2.6.1.96 (characterized)
to candidate RR42_RS27405 RR42_RS27405 aminotransferase

Query= SwissProt::Q84P54
         (515 letters)



>FitnessBrowser__Cup4G11:RR42_RS27405
          Length = 448

 Score =  453 bits (1165), Expect = e-132
 Identities = 218/432 (50%), Positives = 307/432 (71%), Gaps = 1/432 (0%)

Query: 70  LAPFTAGWQSTDVDPLIIEKSEGSHVYDMQGRKYIDTLAGLWCTALGGNEPRLVDAATKQ 129
           L PFT       V PL+I K +G +V D QG++Y++ ++GLWC++LG +  R+++A  + 
Sbjct: 16  LHPFTNLAAHPGVGPLVITKGDGIYVEDDQGKRYLEGMSGLWCSSLGFSHARVIEAGVEA 75

Query: 130 LNTLPFYHSFWNRTTKPSLDLAKELLDMFTAKKMAKAFFTNSGSEANDTQVKLVWYYNNA 189
           + TLP+YH+F +R+   ++ LA++L+ M     M+K FF NSGSEANDT VKLVWYY+NA
Sbjct: 76  MRTLPYYHTFNHRSNPAAIMLAEKLVAMAPVP-MSKVFFANSGSEANDTAVKLVWYYHNA 134

Query: 190 LGRPNKKKFIARAKAYHGSTLISASLTGLPALHQNFDLPAPFVLHTDCPHYWRYHLPGET 249
           +G+P+KKK IAR  AYHG T+ +ASL+GL A H++FDLP   +L   CPH++RY  PGE+
Sbjct: 135 IGKPDKKKIIARTNAYHGVTVAAASLSGLQANHRDFDLPIDRILRAGCPHHYRYGAPGES 194

Query: 250 EEEFSTRLAKNLEDLILKEGPETIAAFIAEPVMGAGGVIPPPATYFDKIQAVVKKYDILF 309
           E  F++RLA+ LE LI  +GP+TI AFIAEPVMGAGGVI PPATYF +IQAV++++DIL 
Sbjct: 195 EAAFASRLAQELEALIQAQGPDTIGAFIAEPVMGAGGVIVPPATYFAEIQAVLRRHDILL 254

Query: 310 IADEVICAFGRLGTMFGSDMYNIKPDLVTLAKALSSAYMPIGAVLVSPEVSDVIHSQSNK 369
           IADEVIC FGR G MFGS  Y ++PD++T AKALSS YMPI AV+VS +V   I + S K
Sbjct: 255 IADEVICGFGRTGAMFGSTTYGMRPDILTCAKALSSGYMPISAVMVSEKVHAAIAANSGK 314

Query: 370 LGSFSHGFTYSGHPVACAVALEAIKIYKERNMVERVNRISPKFQEGLKAFSDSPIIGEIR 429
           +G+F HGFTYSGHPV  AVALE +++Y++  +++ VN I+P+FQ+ L+A++   ++GE+R
Sbjct: 315 IGTFGHGFTYSGHPVTTAVALETLRVYEDDRILDHVNAIAPRFQQALQAYAGRALVGEVR 374

Query: 430 GLGLILATEFANNKSPNDHFPPEWGVGAYFGAQCQKNGMLVRVAGDTIMMSPPFVVTPEE 489
           G+GL+ A E A   +    F P    G       Q+ G++VR  GDTI   PP ++T  +
Sbjct: 375 GVGLLGAIELAAEPAARRAFDPALKAGPRLAQLAQEQGLIVRAMGDTIAFCPPLIITEAQ 434

Query: 490 LDELIRIYGKAL 501
           + EL   + +A+
Sbjct: 435 IGELFARFERAM 446


Lambda     K      H
   0.318    0.135    0.402 

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: 544
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: 515
Length of database: 448
Length adjustment: 34
Effective length of query: 481
Effective length of database: 414
Effective search space:   199134
Effective search space used:   199134
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 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