GapMind for catabolism of small carbon sources

 

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

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_011383255.1 AMB_RS04150 acetylornithine transaminase

Query= BRENDA::Q0K2K2
         (423 letters)



>NCBI__GCF_000009985.1:WP_011383255.1
          Length = 388

 Score =  212 bits (539), Expect = 2e-59
 Identities = 146/401 (36%), Positives = 208/401 (51%), Gaps = 40/401 (9%)

Query: 25  DFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFTHTAYQIVPY 84
           D   ++ E A L   +GR + DF AG+AV   GH HPR++ A+ AQ  +  H +  +   
Sbjct: 14  DVIFEQGEGAWLTASDGRRFLDFGAGVAVNALGHAHPRLVAALEAQAGKLWHCS-NLYRV 72

Query: 85  QGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKIARAH---TGRPG---VIAFSGA 138
            G   +AER   L+     +      TGAEA+E  IKIAR +    GRP    ++A +G+
Sbjct: 73  PGQERVAER---LIKASFADTAFFCNTGAEAMELVIKIARRYHHCAGRPERNRIVACTGS 129

Query: 139 FHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQALEGLFKTDIDP 198
           FHGRT+  +A  G    Y  GFGP      H P+            L+A  G   ++   
Sbjct: 130 FHGRTIATLAAAG-TPKYLEGFGPVAQGFDHVPYGD----------LEAARGAIGSN--- 175

Query: 199 ARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMSHH 258
              AA++VEPVQGEGG + A   ++RGLRA+ DQ G++L+ DEVQTG GRTGK+FA    
Sbjct: 176 --TAALLVEPVQGEGGIRPADPAYLRGLRALADQFGLLLLMDEVQTGIGRTGKLFAHEWS 233

Query: 259 DVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVAAAHAVIDVIEE 318
            + PD++ +AK L GG P+ AV           PG  G T+ GNPLA+A A AV+D +  
Sbjct: 234 GIAPDVMGLAKGLGGGFPVGAVLATEKAASCMTPGTHGCTFGGNPLAMAVAEAVLDEVMA 293

Query: 319 EKLCERSASLGQQLREHL--LAQRKHCPAMAEVRGLGSMVAAEFCDPATGQPSAEHAKRV 376
               ER  ++   LR  L  LA R++  A+A+VRG G M+         G  +       
Sbjct: 294 PGFLERVQAVAALLRGRLDDLA-RRYPGAIAQVRGQGLML---------GLKTVPVNTEF 343

Query: 377 QTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVL 417
             +   AG  LL  G   NV+R + PL I +A+ + A+ ++
Sbjct: 344 NAKLFAAG--LLAVGAGDNVVRLVPPLIIGEAEVERAVEII 382


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: 463
Number of extensions: 22
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: 423
Length of database: 388
Length adjustment: 31
Effective length of query: 392
Effective length of database: 357
Effective search space:   139944
Effective search space used:   139944
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