GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Caulobacter crescentus NA1000

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate CCNA_02244 CCNA_02244 aminotransferase class I family protein

Query= BRENDA::Q72LL6
         (397 letters)



>FitnessBrowser__Caulo:CCNA_02244
          Length = 425

 Score =  305 bits (780), Expect = 2e-87
 Identities = 175/400 (43%), Positives = 240/400 (60%), Gaps = 18/400 (4%)

Query: 6   WSEAFGKGAGRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREK-- 63
           W+  F +   R++AS IRELLKL  +P ILSFAGG+P P LFP +E  +    IL +   
Sbjct: 23  WAGRFSERMSRVRASEIRELLKLLDQPDILSFAGGIPDPGLFPAQEIQKGYDAILADPVL 82

Query: 64  GEVALQYSPTEGYAPLRAFVAE-----WIGVRPEEVLITTGSQQALDLVGKVFLDEGSPV 118
              ALQYS +EGY PLR ++AE      +   P+ +++T GSQQALDL+GK+FL +G  V
Sbjct: 83  SRQALQYSVSEGYLPLRQWIAERMTRDGMPCGPDNIMLTAGSQQALDLIGKLFLTKGDTV 142

Query: 119 LLEAPSYMGAIQAFRLQGPRFLTVP--AGEEGPDLDALEEVLKRERPRFL-YLIPSFQNP 175
           ++  P+Y+GA+QAF    P +L +P  A  +G D  AL   +    PR L Y +P F NP
Sbjct: 143 MVARPTYLGALQAFNGYEPAYLDLPETALSQGVDEAAL---MAGRAPRPLGYFVPDFANP 199

Query: 176 TGGLTPLPARKRLLQMVMERGLVVVEDDAYRELYFGEARLPSLF--ELAREAGYPGV--I 231
           TG    L  R+ LL M     + +VED AYREL F     P++   ++ R  G      +
Sbjct: 200 TGVSLTLAEREALLAMADRLDMTLVEDAAYRELRFAGEATPTVLGLDITRSGGIDNARTL 259

Query: 232 YLGSFSKVLSPGLRVAFAVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEGFSERLE 291
           +LG+ SK LSP LR+ +       ++KLV  KQGADLH   +NQM+ H  + EG+ + L 
Sbjct: 260 FLGTLSKTLSPALRIGWVCGPKAVIEKLVLLKQGADLHVSTINQMVAHRAVTEGYDQHLH 319

Query: 292 RVRRVYREKAQAMLHALDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRAL-EENVA 350
           R+R  Y  KA+ ML AL+R +PK V ++ P+GGMFVW++LP+G+    L  RA+ EE VA
Sbjct: 320 RLRGAYGAKARVMLAALERTMPKGVTWSHPEGGMFVWIDLPEGIDGAALLARAIEEERVA 379

Query: 351 FVPGGPFFANGGGENTLRLSYATLDREGIAEGVRRLGRAL 390
           FVPG PFFA     N +RLSY+      I EGV+RL R +
Sbjct: 380 FVPGAPFFAENQTPNAIRLSYSLPTDAQIEEGVQRLARLI 419


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: 481
Number of extensions: 23
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: 425
Length adjustment: 31
Effective length of query: 366
Effective length of database: 394
Effective search space:   144204
Effective search space used:   144204
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 Aug 03 2021. The underlying query database was built on Aug 03 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