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_083763404.1 AMB_RS01605 aspartate aminotransferase family protein

Query= BRENDA::Q0K2K2
         (423 letters)



>NCBI__GCF_000009985.1:WP_083763404.1
          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.

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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