GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Magnetospirillum magneticum AMB-1

Align 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized)
to candidate WP_011383255.1 AMB_RS04150 acetylornithine transaminase

Query= SwissProt::P50457
         (421 letters)



>NCBI__GCF_000009985.1:WP_011383255.1
          Length = 388

 Score =  207 bits (526), Expect = 6e-58
 Identities = 146/399 (36%), Positives = 204/399 (51%), Gaps = 44/399 (11%)

Query: 27  QSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFTHTA--YQIVPYES 84
           +  E A L   +G  ++DF AG+AV   GH HP LVAA+E Q  +  H +  Y++   E 
Sbjct: 18  EQGEGAWLTASDGRRFLDFGAGVAVNALGHAHPRLVAALEAQAGKLWHCSNLYRVPGQER 77

Query: 85  YVTLAEKINALAPVSGQAKTAFF-TTGAEAVENAVKIARAH---TGRPG---VIAFSGGF 137
              +AE++      +  A TAFF  TGAEA+E  +KIAR +    GRP    ++A +G F
Sbjct: 78  ---VAERLIK----ASFADTAFFCNTGAEAMELVIKIARRYHHCAGRPERNRIVACTGSF 130

Query: 138 HGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQDSLDAIERLFKSDIEAK 197
           HGRT  T+A  G    Y  GFGP      HVPY            L+A      S+    
Sbjct: 131 HGRTIATLAAAG-TPKYLEGFGPVAQGFDHVPY----------GDLEAARGAIGSN---- 175

Query: 198 QVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMDHYA 257
             AA++ EPVQGEGG   A    +  +R L D+ G++++ DEVQ+G  RTGKLFA +   
Sbjct: 176 -TAALLVEPVQGEGGIRPADPAYLRGLRALADQFGLLLLMDEVQTGIGRTGKLFAHEWSG 234

Query: 258 DKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNIIDKE 317
             PD+M +AK L GG P+  V+          PG  G T+ GNPLA+A A AVL+ +   
Sbjct: 235 IAPDVMGLAKGLGGGFPVGAVLATEKAASCMTPGTHGCTFGGNPLAMAVAEAVLDEVMAP 294

Query: 318 SLCERANQLGQRLKNTLIDAKESVP-AIAAVRGLGSMIAVEFNDPQTGEPSAAIAQKIQQ 376
              ER   +   L+  L D     P AIA VRG G M+         G  +  +  +   
Sbjct: 295 GFLERVQAVAALLRGRLDDLARRYPGAIAQVRGQGLML---------GLKTVPVNTEFNA 345

Query: 377 RALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKIL 415
           +  A GLL +  GA  NV+R + PL I +A+ + A++I+
Sbjct: 346 KLFAAGLLAV--GAGDNVVRLVPPLIIGEAEVERAVEII 382


Lambda     K      H
   0.319    0.134    0.388 

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: 436
Number of extensions: 25
Number of successful extensions: 6
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: 421
Length of database: 388
Length adjustment: 31
Effective length of query: 390
Effective length of database: 357
Effective search space:   139230
Effective search space used:   139230
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 (21.8 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