GapMind for catabolism of small carbon sources

 

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

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_083763404.1 AMB_RS01605 aspartate aminotransferase family protein

Query= BRENDA::Q9I6M4
         (426 letters)



>NCBI__GCF_000009985.1:WP_083763404.1
          Length = 384

 Score =  226 bits (576), Expect = 9e-64
 Identities = 148/412 (35%), Positives = 214/412 (51%), Gaps = 55/412 (13%)

Query: 29  ERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTC--FQVLAYEP 86
           ER E + ++  +GR Y+DFA G+AV   GH HP+++ A+  Q  K+ HT   ++V   E 
Sbjct: 12  ERGEGAYLFTADGRRYLDFAAGVAVNALGHCHPRLVKALTAQAAKVWHTSNLYRVAGQES 71

Query: 87  YIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARAATGRAG------VIAFTGAYH 140
                   AK V   F        SG+EA+E ++K+AR     AG      +I   GA+H
Sbjct: 72  VA------AKLVERSFADTVFFCNSGAEALECSIKMARRHHFAAGNPQRYRIICAEGAFH 125

Query: 141 GRTMMTLGLTGK------VVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKN 194
           GRT+ T+   G+        P   G   +P G   AL              ASI      
Sbjct: 126 GRTLATVAAGGQKKHLEGFAPAVDGFDHVPYGNLNALR-------------ASIT----- 167

Query: 195 DAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFA 254
               ++ AAI++EPVQGEGG       +++RLRA  D+ G+LLI DEVQTG GRTGT FA
Sbjct: 168 ----EETAAILVEPVQGEGGIVPGDPDYLRRLRATADEFGLLLIFDEVQTGMGRTGTLFA 223

Query: 255 TEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLK 314
            EQ GI PD+   AK +GGGFP+       +    + PG  G T+ G+P+A A A  VL 
Sbjct: 224 HEQAGIAPDIMGVAKGLGGGFPVGACLATTKAASGMVPGTHGSTFGGNPLAMAVAGEVLD 283

Query: 315 VFEEEKLLERSQAVGERLKAGLREIQAKHK-VIGDVRGLGSMVAIELFEGGDTHKPAAEL 373
           +  E   LE  QA+   L++ + +  A+   V+ +VRGLG M+ I+         P  E+
Sbjct: 284 IMAEPGFLEHVQAMAALLRSKVEDTAARFPGVVEEVRGLGLMLGIK------PRMPNTEM 337

Query: 374 VSKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAECFDEL 425
           V+++     E GL+ +  G   N++R L P+ I DAQ+++ + ILA  FDE+
Sbjct: 338 VARLA----EGGLLTVGAGD--NIVRLLPPLIINDAQVDEAVGILARAFDEV 383


Lambda     K      H
   0.319    0.137    0.393 

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: 424
Number of extensions: 14
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: 426
Length of database: 384
Length adjustment: 31
Effective length of query: 395
Effective length of database: 353
Effective search space:   139435
Effective search space used:   139435
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