GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Dyella japonica UNC79MFTsu3.2

Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate N515DRAFT_1410 N515DRAFT_1410 methionine aminotransferase

Query= SwissProt::P58350
         (410 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1410
          Length = 381

 Score =  161 bits (407), Expect = 3e-44
 Identities = 114/367 (31%), Positives = 175/367 (47%), Gaps = 28/367 (7%)

Query: 46  LGAGEPDFDTPEHVKQAASDAIHRGETKYTALDGTPELKKAIREKFQRENGLAYEL-DEI 104
           LG G PDF+ P+ +++A + A+  G  +Y    G P L++ I  K +R  G   +   E+
Sbjct: 30  LGQGFPDFEPPQALREAIARAMAEGRNQYAPGIGLPTLREQIALKTERMYGRRIDAAGEV 89

Query: 105 TVATGAKQILFNAMMASLDPGDEVIIPTPYWTSYSDIVHICEGKPVLIACDASSGFRLTA 164
           TV +GA + LF A+ A +  GDEVI+  P + SY  ++ +   K V I     S F +  
Sbjct: 90  TVTSGATEALFAAIAAVVRAGDEVIVFDPAYDSYEPVIELQGAKAVHIPLTVPS-FGVDW 148

Query: 165 EKLEAAITPRTRWVLLNSPSNPSGAAYSAADYRPLLEVLLRHPHVWLLVDDMYEHIVYDG 224
           +++  A+TPRTR +L+NSP NPSGA  SAAD    L  ++R   + +L D++YEHIV+DG
Sbjct: 149 QRVRDAVTPRTRMILINSPHNPSGAVLSAADL-DQLAAIVRDTEIVVLSDEVYEHIVFDG 207

Query: 225 FRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGWRIGYAGGPRELIKAMAVVQSQATSCPSS 284
               +  +    L  R++ V+   K Y  TGW++GYA  P  L      V    T C   
Sbjct: 208 ALHQSVLR-HAELAARSIVVSSFGKTYHCTGWKLGYAVAPAALSAEFRKVHQYLTFCTFH 266

Query: 285 ISQAASVAALNGPQDFLKERTESFQRRRDLVVNGLNAIDGLDCRVPEGAFYTFSGCAGVL 344
            +Q A    +    +   E    +Q +R          D     +    F       G  
Sbjct: 267 PAQVAFAEFMASTPEHYLELPAFYQAKR----------DRFRALIAPSRFKLLDVPGGYF 316

Query: 345 GKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGSAFGLSPFF---------RISYATSEAEL 395
             V  S  R + D  FC +L++   VA +P     L+PF+         R+ +A S+A +
Sbjct: 317 QLVDYSAIRDEPDVTFCEWLVKQGGVAAIP-----LAPFYETAPDTRLVRLCFAKSDATM 371

Query: 396 KEALERI 402
             A ER+
Sbjct: 372 DAAAERL 378


Lambda     K      H
   0.318    0.134    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: 352
Number of extensions: 27
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: 410
Length of database: 381
Length adjustment: 31
Effective length of query: 379
Effective length of database: 350
Effective search space:   132650
Effective search space used:   132650
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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