GapMind for catabolism of small carbon sources

 

Aligments 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_083763404.1 AMB_RS01605 aspartate aminotransferase family protein

Query= BRENDA::Q0K2K2
         (423 letters)



>lcl|NCBI__GCF_000009985.1:WP_083763404.1 AMB_RS01605 aspartate
           aminotransferase family protein
          Length = 384

 Score =  215 bits (548), Expect = 2e-60
 Identities = 149/406 (36%), Positives = 205/406 (50%), Gaps = 38/406 (9%)

Query: 25  DFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFTHTAYQIVPY 84
           D   +R E A L+  +GR Y DFAAG+AV   GH HPR+++A+ AQ  +  HT+  +   
Sbjct: 8   DLAFERGEGAYLFTADGRRYLDFAAGVAVNALGHCHPRLVKALTAQAAKVWHTS-NLYRV 66

Query: 85  QGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKIARAH---TGRPG---VIAFSGA 138
            G  ++A +   LV     +      +GAEA+E +IK+AR H    G P    +I   GA
Sbjct: 67  AGQESVAAK---LVERSFADTVFFCNSGAEALECSIKMARRHHFAAGNPQRYRIICAEGA 123

Query: 139 FHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQALEGLFKTDIDP 198
           FHGRTL  +A  G+    + GF P      H P+ +          L AL      +   
Sbjct: 124 FHGRTLATVAAGGQKKHLE-GFAPAVDGFDHVPYGN----------LNALRASITEE--- 169

Query: 199 ARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMSHH 258
              AAI+VEPVQGEGG      D++R LRA  D+ G++LI DEVQTG GRTG +FA    
Sbjct: 170 --TAAILVEPVQGEGGIVPGDPDYLRRLRATADEFGLLLIFDEVQTGMGRTGTLFAHEQA 227

Query: 259 DVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVAAAHAVIDVIEE 318
            + PD++ +AK L GG P+ A           +PG  G T+ GNPLA+A A  V+D++ E
Sbjct: 228 GIAPDIMGVAKGLGGGFPVGACLATTKAASGMVPGTHGSTFGGNPLAMAVAGEVLDIMAE 287

Query: 319 EKLCERSASLGQQLREHLLAQRKHCPAMA-EVRGLGSMVAAEFCDPATGQPSAEHAKRVQ 377
               E   ++   LR  +       P +  EVRGLG M+  +   P T          + 
Sbjct: 288 PGFLEHVQAMAALLRSKVEDTAARFPGVVEEVRGLGLMLGIKPRMPNT---------EMV 338

Query: 378 TRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALAE 423
            R  E G  LLT G   N++R L PL I  AQ D A+ +L +A  E
Sbjct: 339 ARLAEGG--LLTVGAGDNIVRLLPPLIINDAQVDEAVGILARAFDE 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: 447
Number of extensions: 23
Number of successful extensions: 5
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: 384
Length adjustment: 31
Effective length of query: 392
Effective length of database: 353
Effective search space:   138376
Effective search space used:   138376
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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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