GapMind for catabolism of small carbon sources

 

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

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate N515DRAFT_1217 N515DRAFT_1217 transcriptional regulator, GntR family

Query= BRENDA::Q72LL6
         (397 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1217
          Length = 468

 Score =  183 bits (465), Expect = 8e-51
 Identities = 125/388 (32%), Positives = 197/388 (50%), Gaps = 11/388 (2%)

Query: 15  GRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVALQYSPTE 74
           G +    ++E+L +  R  +L      P+P L P+     A +R LR      L Y+P +
Sbjct: 85  GAVNNPALQEVLDMLARSDVLPLHSATPSPALLPQAALTAALSRSLRHHPAAVLDYAPPQ 144

Query: 75  GYAPLRAFVAE-----WIGVRPEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAI 129
           G   LR  +A         V P+E++IT G+ + + L  +   + G  VL+E P+Y G +
Sbjct: 145 GLPALRRQIARRYAQLGAAVSPDEIVITAGAMEGISLALRTLAEPGDVVLVETPTYHGIL 204

Query: 130 QAFRLQGPRFLTVP-AGEEGPDLDALEEVLKRERPRFLYLIPSFQNPTGGLTPLPARKRL 188
           QA      + L VP    +G D+  L+++L++ R R   L+P+F NP G +T   A++ L
Sbjct: 205 QAVAALRLKVLEVPNLPGQGIDVARLDQLLQQNRVRAAVLVPNFNNPLGSVTGDAAKQAL 264

Query: 189 LQMVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPGVIYLGSFSKVLSPGLRVAF 248
           L      G VV+EDD Y +L +   R PS   L R      +I  GSFSK LSPGLR+ +
Sbjct: 265 LASCARHGTVVIEDDVYGDLAWSGER-PS--PLRRWDTRGNLISCGSFSKSLSPGLRLGW 321

Query: 249 AVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEGFSER-LERVRRVYREKAQAMLHA 307
            +A       LV+AK  + +    L Q+ + E L++   ER L R+RR   + AQ +  A
Sbjct: 322 -IAAGAWTDALVRAKYFSTVGAASLPQLAMAEYLQKHDLERHLRRLRRALADNAQRLHEA 380

Query: 308 LDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGENTL 367
           + R  P   R + P+GG+ +W++LP+G   + LF  ALE+ +   PG  F + G   + L
Sbjct: 381 ISRHWPAGTRASEPRGGLSLWLQLPEGGDGQMLFEAALEQGIGTSPGVLFSSRGDYGDCL 440

Query: 368 RLSYATLDREGIAEGVRRLGRALKGLLA 395
           RLS        + + +++LG+     LA
Sbjct: 441 RLSCGMPWDARLEQALKKLGQLAARQLA 468


Lambda     K      H
   0.320    0.139    0.403 

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: 459
Number of extensions: 25
Number of successful extensions: 6
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: 397
Length of database: 468
Length adjustment: 32
Effective length of query: 365
Effective length of database: 436
Effective search space:   159140
Effective search space used:   159140
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: 51 (24.3 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 (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