GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Caulobacter crescentus NA1000

Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate CCNA_02244 CCNA_02244 aminotransferase class I family protein

Query= reanno::azobra:AZOBR_RS06555
         (404 letters)



>FitnessBrowser__Caulo:CCNA_02244
          Length = 425

 Score =  400 bits (1027), Expect = e-116
 Identities = 204/400 (51%), Positives = 272/400 (68%), Gaps = 6/400 (1%)

Query: 4   DWGNVFAGRVAGMGASEIRELLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQSNS 63
           DW   F+ R++ + ASEIRELLKLL++P+I+SFAGGIPDP  FP   I + Y+ I     
Sbjct: 22  DWAGRFSERMSRVRASEIRELLKLLDQPDILSFAGGIPDPGLFPAQEIQKGYDAILADPV 81

Query: 64  GAGGALQYTISEGFTPLREWICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGPGEK 123
            +  ALQY++SEG+ PLR+WI   + R G+  G D +++T+GSQQAL+ +GKL +  G+ 
Sbjct: 82  LSRQALQYSVSEGYLPLRQWIAERMTRDGMPCGPDNIMLTAGSQQALDLIGKLFLTKGDT 141

Query: 124 ILVTRPTYLGALQAFSPYEPQYLSVPGDA--EGPDLAAVEAALEQKPKFFYLVPDFQNPN 181
           ++V RPTYLGALQAF+ YEP YL +P  A  +G D AA+ A    +P   Y VPDF NP 
Sbjct: 142 VMVARPTYLGALQAFNGYEPAYLDLPETALSQGVDEAALMAGRAPRP-LGYFVPDFANPT 200

Query: 182 GTTISLARREALLDLCAKHGVPIVEDAAYTELRYEGEPIPSMVALDAARNGGKITNV--L 239
           G +++LA REALL +  +  + +VEDAAY ELR+ GE  P+++ LD  R+GG I N   L
Sbjct: 201 GVSLTLAEREALLAMADRLDMTLVEDAAYRELRFAGEATPTVLGLDITRSGG-IDNARTL 259

Query: 240 FCGSFSKTMVPALRVGWINGPAEVINRLVLMKQAGDLHTSTINQIVLHDVVSQNFDSHIR 299
           F G+ SKT+ PALR+GW+ GP  VI +LVL+KQ  DLH STINQ+V H  V++ +D H+ 
Sbjct: 260 FLGTLSKTLSPALRIGWVCGPKAVIEKLVLLKQGADLHVSTINQMVAHRAVTEGYDQHLH 319

Query: 300 RLRAGYKERRDAMLTALSEFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANVA 359
           RLR  Y  +   ML AL    P GVTW+ PEGGMFVWI+LPEG DG  LLARAI++  VA
Sbjct: 320 RLRGAYGAKARVMLAALERTMPKGVTWSHPEGGMFVWIDLPEGIDGAALLARAIEEERVA 379

Query: 360 FVPGSAFHADRSGKNTLRLSFSNNNPERIREGIRRLCGLL 399
           FVPG+ F A+    N +RLS+S     +I EG++RL  L+
Sbjct: 380 FVPGAPFFAENQTPNAIRLSYSLPTDAQIEEGVQRLARLI 419


Lambda     K      H
   0.320    0.138    0.410 

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: 525
Number of extensions: 25
Number of successful extensions: 3
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: 404
Length of database: 425
Length adjustment: 31
Effective length of query: 373
Effective length of database: 394
Effective search space:   146962
Effective search space used:   146962
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.

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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