GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Luteimonas huabeiensis HB2

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_024888968.1 Z164_RS0101410 AMP-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_3009
         (578 letters)



>NCBI__GCF_000559025.1:WP_024888968.1
          Length = 507

 Score =  150 bits (378), Expect = 2e-40
 Identities = 149/545 (27%), Positives = 231/545 (42%), Gaps = 63/545 (11%)

Query: 31  IGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHN 90
           +G  F   V R PE  AL  V    R  YA        + + L   G+  GD V     N
Sbjct: 4   LGTTFLAAVERDPE--ALAIVDGDVRLDYAAWYHAISSVVAGLEAAGVKRGDHVVSVLRN 61

Query: 91  NAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLREL 150
             E   +  A    G +LV +N      +V + ++    + +V                 
Sbjct: 62  RWEAATLHWACQFAGAILVPLNWRATAEDVAFCVHDSEARAIV----------------- 104

Query: 151 APEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVA 210
              ++      + AA L      V +D       D  G  RF + +A     D   AQ  
Sbjct: 105 ---YEDAPAKAIAAAGLDDAVLHVTLD------VDRAGAQRFGDWLA----VDAPPAQPL 151

Query: 211 AGLQATDPINIQFTSGTTGFPKGATLTHR--------NILNNGFFIGECMKLTPADRLCI 262
           A   A D   + +TSGTT  PKG    HR        +I  N +  G         R   
Sbjct: 152 A--VAEDWSLMLYTSGTTSKPKGVPRRHRAERAAAIAHIAQNRYRNGA--------RTLG 201

Query: 263 PVPLYHCFGMVLGNLAC-FTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAEL 321
            +PLYH  G V   LAC   +G  +  P   FD    L+ +  ER   L+ VPT++   L
Sbjct: 202 VMPLYHTMG-VRSLLACALLNGTFVCLPK--FDAGQALRLIAAERIDNLYLVPTLYHDLL 258

Query: 322 DHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDT 381
            HP FA  ++ ++RT   AG+     +++++            YG +E    + +    +
Sbjct: 259 QHPDFAATDIGSVRTLGFAGASMTDGLLQKLQAAFAPELFVNHYGSSEIYTFTIEDDAPS 318

Query: 382 -PLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCT--KGYSVMHGYWGDEAKTRE 438
            P S   S + Q+   + +   D  T A     + G+      G     GYW       +
Sbjct: 319 KPGSAGRSGLNQMVRVVPLDATDAHTRAAP--NEEGQIVALLAGDEAFEGYWRRPDADAK 376

Query: 439 AIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVV 498
           A+  GGW  TGD   +D +G + + GR+ DM+I GGEN+ P EIE  L  HP+V +V VV
Sbjct: 377 AL-RGGWYFTGDTGYVDEDGDLFVTGRVDDMIISGGENVSPVEIESHLSLHPRVGEVAVV 435

Query: 499 GVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCK-GQIAHYKVPRYIRFVTSFPMTVTGKI 557
           G+PD+++G  + A++  +     TED++ A+C+  ++A++K PR   FV   P +  GK+
Sbjct: 436 GLPDERWGSVVTAFV--RRNGPVTEDELDAWCRDSKLANFKRPRRFVFVEDIPKSPVGKL 493

Query: 558 QKFKI 562
            + K+
Sbjct: 494 LRRKL 498


Lambda     K      H
   0.320    0.136    0.412 

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: 636
Number of extensions: 32
Number of successful extensions: 4
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: 578
Length of database: 507
Length adjustment: 35
Effective length of query: 543
Effective length of database: 472
Effective search space:   256296
Effective search space used:   256296
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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